On a Monday morning in early September, Hildegard Stoecker was on her front patio in southwest Tucson, where she likes to spend the sunrise. In a few hours, the sun would beat hard on the Arizona desert and temperatures would hit 100 degrees. But at 6 a.m., it was cool. A soft glow illuminated the peaked foothills of Tucson Mountain Park behind her home; in her front yard, cacti and Caesalpinia bushes were bathed in pink light and a hummingbird hovered by the window.

Stoecker was not feeling serene. On Friday she had received a message about a man on Arizona’s death row, whose name was all too familiar. Barry Lee Jones was convicted in 1995 for the rape and murder of a young girl. It was the kind of unfathomable crime that Stoecker felt should send someone to hang “from the highest tree,” she recalled. The trial judge agreed and sentenced Jones to die.

But 22 years later, Stoecker was disturbed to hear that Jones was still on death row. Not because she thought he should have been executed by now. In fact, it was the opposite: She had mistakenly assumed he’d probably been removed from death row — maybe even exonerated. “What you’re saying bothers me quite a bit,” she said. The sentiment was surprising coming from Stoecker. She was one of the jurors who convicted Jones.

Some 10 years ago, she explained, an investigator with the Arizona Federal Public Defender’s Office had visited her at home. He was interviewing trial jurors as part of the appellate process in Jones’s case. Her memory of the meeting is vague. But it made a strong impression, bringing up old doubts about the evidence presented at trial. She had always felt that Jones’s lawyers did a poor job representing him. The meeting made her think there had been other flaws in his case — and the state would be forced to address them.

Stoecker is in her 70s, with cropped gray hair. She wore jeans and a T-shirt with a bald eagle on it and was barefoot, seated in her motorized wheelchair. Decades ago, she was diagnosed with an incurable lung condition she contracted while working at a ceramics plant. At the time of Jones’s trial, she had just begun her treatment and was increasingly unable to work. She got involved in animal welfare. That morning, her rescue cockatoo, Max, squawked insistently from inside the house. Stoecker explained that Max had been traumatized after seeing “a bird friend” killed by dogs and had plucked out his own feathers. She was fostering him until he found a new home.

If Stoecker’s natural compassion made her an unlikely death penalty supporter, Jones’s sentence had not been for her to decide. In those years, judges, not juries, imposed the death penalty in Arizona. “Whether we as a jury would’ve sentenced him to death, I don’t know,” she said. But there was another reason capital punishment made Stoecker uneasy. When she was a teenager in San Francisco during the 1950s, California executed a man named Burton Abbott for raping and murdering a 14-year-old girl. Abbott swore he was innocent; like Jones, his conviction relied heavily on circumstantial evidence. On the day he died, the governor called the prison to grant a last-minute stay, only to find the execution was already underway.

“I don’t know that I was fully convinced he was guilty,” Stoecker said about Abbott. But she was only in high school — “What did I know?” She did not give the death penalty much thought after that. Not until the trial of Barry Jones.

“This is something that’s been with me for a long, long time,” Stoecker said. The possibility that she might have made the wrong decision distressed her.

“I realize a lot of people just put it out of their minds and go on with their lives,” she said. A friend had told her, “‘Look, you did the best you could at the time. You know, just kinda let it go.’ And I can’t let it go.”

Barry Lee Jones, 35, on the day of his interrogation and arrest at the Pima County Sheriff’s Department.

Since the day of his arrest in 1994, Barry Lee Jones has insisted he did not rape or kill his girlfriend’s 4-year-old daughter, Rachel Yvonne Gray. Jailed on the same day the child’s lifeless body arrived at a Tucson hospital, Jones admitted she’d been injured on his watch, repeatedly saying she had fallen from his parked yellow work van the day before, hitting her head. Jones said Rachel told him a little boy had pushed her out. But even if it was true, that did not explain the bruises covering her body, or the abdominal injury that took her life.

Almost no physical evidence linked Jones to Rachel’s injuries — and there was nothing to show he was guilty of rape. But when children die under mysterious circumstances, early suspicion typically falls on the adults who were closest to them in their final hours. On that day, witnesses said, that person was Jones. He and Rachel’s mother, Angela Gray, were tried back to back in 1995; Gray was convicted of child abuse but acquitted of murder. Jones was sentenced to die.

After more than 20 years insisting upon his innocence, Jones won a rare evidentiary hearing from a U.S. district judge, set to begin October 30. Attorneys with the Arizona Federal Public Defender’s Office plan to argue that Jones’s trial was fundamentally unfair, marred by ineffective assistance of counsel in violation of his Sixth Amendment rights. Moreover, they say, bad lawyering at the post-conviction level left the trial attorneys’ failures unaddressed, resulting in a horrible miscarriage of justice. If his lawyers succeed, Jones could win a new trial — or even be released from prison.

Poor defense representation and a lack of physical evidence are both hallmarks of wrongful convictions. The files in Jones’s case reveal many more. They show a rush to judgment, tunnel vision by the Pima County Sheriff’s Department, and a shifting theory of the crime by the state. Prosecutors relied on the most dubious kinds of evidence, from flawed forensics to the eyewitness accounts of young children. Vital pieces of evidence were lost, concealed, or never collected to begin with. More recently, DNA testing on one key item has failed to implicate Jones.

In a state where eight people have been exonerated from death row, Arizona prosecutors have fought against reopening Jones’s case, even as the basis for his conviction has fallen apart. As his defense attorneys argue, “Jones was convicted based on a very specific timeline, which was grounded on a single factual premise: that Rachel was fatally injured and sexually assaulted while she was alone with Jones on portions of Sunday, May 1, 1994.” The total time frame was no longer than four hours, during which Jones was seen taking the child on short trips in his van. But several medical experts hired by defense attorneys have concluded that Rachel’s fatal injury could not possibly have occurred within the narrow window presented by the state.

More significant still, in a recent letter to Jones’s lawyers, the Arizona Attorney General’s Office conceded that the current Pima County medical examiner “did not dispute the conclusions of your experts.” And the forensic pathologist who took the stand against Jones in 1995 has acknowledged that his testimony was flawed. Jones’s attorneys are certain that if the case were tried again, “no juror acting reasonably would ever find Jones guilty beyond a reasonable doubt.”

For his part, Jones admits he was no upstanding citizen before he went to prison. But he did not kill Rachel Gray. “I was guilty of a lifestyle,” Jones told me. “I was a thief. I was a dope fiend. … I wasn’t looking out for nobody but myself. And I hold myself responsible, because she died under my roof, on my watch. … I blame myself every day for that.”

The Desert Vista Trailer Park on East Benson Highway in 1994.

It was 6:16 a.m. on May 2, 1994, when 30-year-old Angela Gray arrived in her nightgown at Kino Community Hospital in south Tucson, carrying her youngest child, Rachel. The frail 4-year-old wore pink pajamas with feet. She was pale and had no pulse. Emergency room doctor Steven Seifert was nearing the end of his overnight shift when he entered the examination room. He quickly realized there was nothing to be done. The child was cool to the touch, he would later testify, and rigor mortis had already begun to set in. “She was essentially dead on arrival.”

She was also covered in injuries. There were abrasions and bruises all over her body, Seifert testified, along with other disturbing signs of trauma. Seifert told Gray that her daughter was deceased. Then, as he was obligated to do under the law, he called the police.

Tucson police officer Richard Law was the first to arrive at the hospital. “It was my opinion that, just from looking at her, she had been severely beaten,” he later said in an interview with defense attorneys. He approached Gray, but she was not all there, seemingly fixated on smoking a cigarette. She was thin, with dirty blond hair, and covered with a blanket. Gray told Law that her boyfriend, Barry Jones, had dropped her and Rachel off at the hospital. He supposedly was going to check on the children they had left at home, but he had not come back yet. “I just thought it was very strange,” Law said.

At 7:44 a.m., a second Tucson police officer, Michael Thomson, took a formal statement from Gray in the doctor’s lounge. Gray said that she and her three children lived with Jones and his daughter in the Desert Vista Trailer Park on East Benson Highway, just 4 miles south. The two had met a few months earlier. Jones was a mechanic, Gray said. She did not know his birthday. “Um, um, he’s like 35 years old.”

Gray had no explanation for what had happened to her daughter. She had slept through the previous day, she said, and did not wake up until early evening. “I can tell you what I was told happened,” Gray said. When she woke up, Jones told her that he had put Rachel down for a nap; she had been playing with some kids in his van when she fell out of the vehicle, hitting her head. Jones reassured her that Rachel was OK. But later, she saw Jones returning in his van with Rachel. He said her head had started bleeding, and he had taken her to the fire station just down the street. Paramedics had taken out her braids and rinsed her head, reassuring Jones that head wounds bleed a lot.

Rachel seemed OK, but later she began vomiting, Gray said. Rachel said she was thirsty, but “every time I’d give her a drink, she’d, like, drink it real fast and throw up.” Later that night, she noticed bruises on her chest. Gray said she asked Rachel if someone had hurt her, “and she said the little boys that pushed her out of the van.”

Rachel went to sleep in the bed Gray shared with Jones. The next morning, Gray found her in her own room, buried under the covers. When she removed the sheets, Rachel would not wake up. Gray yelled for Jones. “I remember screaming that we didn’t have time,” she said, “and to just get me to the hospital, and he could come back and get the kids.”

But Jones had not come back to the hospital. “I mean, why wouldn’t he come back?”

Thomson asked Gray about her relationship with Jones. Had he ever hit her? Gray said no. Thomson asked how they disciplined the kids and Gray chuckled. “If the girls would get in trouble for something, it’s ‘You have to stay in your room over this weekend, no TV’ and stuff, and that usually lasts for two or three hours, and he lets them out of the room.” With her son, Jones sometimes took away video games, she said. But Jones was gone a lot and wasn’t usually in charge of the children. “I’ve never seen him lay a hand on any of the kids.”

It was shortly after 8 a.m. when Pima County Sheriff’s Detective Sonia Pesqueira — known then as Sonia Rankin — arrived at Kino Hospital. Thirty-one years old and five months pregnant, Pesqueira had started her career as a campus police officer at Pima Community College, coordinating the rape prevention program. She joined the sheriff’s department in 1984. Her personnel file would show an early passion for investigating sex crimes. One retired detective who worked on the Jones case told me Pesqueira was “top notch,” a zealous defender of children.

Thomson told Pesqueira what he’d learned. From that point on, the investigation belonged to Pesqueira and the Pima County Sheriff’s Department.

An autopsy was scheduled for the next day, but Pesqueira didn’t wait to speak to any doctors. “I do my own examination,” she would later tell a grand jury. “Medical personnel are not in the room.” Pesqueira removed Rachel from the body bag. “I observed numerous and varied contusions on the victim’s torso area to include the abdominal and upper chest area,” she wrote in a report. “There were contusions to the face area, eyes and forehead. The contusions to the area around both eyes appeared to be in varying stages.” There was dried blood on Rachel’s head. Then Pesqueira checked between her legs. There was “extensive injury” inside her vagina, she found. There was also blood.

Pesqueira put Rachel’s pajamas and underwear in a paper bag. Then she went to find Angela Gray.

Traffic on Interstate 10 east of Casa Grande, Ariz., on Dec. 23, 1999.

East Benson Highway cuts a southeast line across Tucson. In its heyday, it was the city’s main drag, lined with “snowbird motels,” cheap roadside lodging with iconic neon signs that attracted Northerners in winter. But along the 5-mile stretch that was home to the Desert Vista Trailer Park, Interstate 10 was built parallel to the road, cutting it off from traffic and isolating its businesses. The area took a turn for the worse. “To most Tucsonans now,” the Arizona Daily Star reported in 2006, “Benson Highway is just a seedy stretch of road on the way to the airport, a place to punch the door-lock button if they hit a red light.”

The Desert Vista was located toward the end of the highway, where rolling desert attracted people who lived off the grid, forming makeshift transient camps. The area could be dangerous. The year after Rachel Gray died, a 20-year-old woman was found raped and strangled at a nearby camp.

Pima County Sheriff’s Detective George Ruelas arrived at the trailer park on the morning of May 2. At around 8:40 a.m., according to his report, Ruelas went to the Rural Metro Fire Station, where Jones told Gray a paramedic had examined Rachel the day before. The station log for Sunday, May 1 “showed no record of contact with Rachel Gray,” Ruelas wrote. The fire captain told Ruelas that as far as he knew, no one there had encountered the little girl.

Jones had lied to his girlfriend.

By the time Ruelas sat down with Jones’s 11-year-old daughter, Brandie, later that morning, rumors were flying at the Desert Vista. Police had found her father at a transient camp nearby. Their home had also been searched. The single-wide trailer was surrounded by junk: old tires, slabs of wood, and large appliances scattered in front of the chain-link fence. Inside it was dirty and cluttered, with pockmarked wood paneling covering the walls.

“I have a question to ask,” Brandie said. “Um, what kid did my dad hurt?” Ruelas said he did not know if Jones had hurt any kid. “’Cause that’s what everyone’s tellin’ me,” Brandie said, but “my dad didn’t hurt any kids.”

The yellow work van driven by Barry Jones. The inside was divided into compartments filled with tools.

Brandie remembered hearing Rachel say she had fallen from the van. The vehicle’s large interior was filled with tools, divided into compartments and covered with a piece of plywood. Brandie explained that there weren’t any kids Rachel’s age at the trailer park, so she liked to hang out while Jones did mechanical work. “She’ll say, Oh, you got that crooked, and he’ll have to go back over it, and they, like, have a lot of fun together,” Brandie said.

Brandie told Ruelas that Jones did not hit her, Gray, or any of the kids. She also shared another thing: On Sunday, Rachel said that a boy had hit her in the stomach with a metal bar the day before. A misunderstanding ensued — Gray thought Rachel meant that Jones had hit her, and the two got into an argument. But Rachel meant a little boy, Brandie said. She did not know who Rachel was talking about. But she did see a bruise on Rachel’s stomach.

Meanwhile, another detective was talking to Becky, Rachel’s 10-year-old sister, at the sheriff’s department. Becky said that she had come back from a friend’s house Sunday evening and saw Rachel on the couch, with a washcloth on her head. Her mother asked Rachel how she got injured, and “she kept saying, A boy pushed me out of the van and hit me with a metal bar in the stomach,” Becky said.

The detective asked Becky if she thought Jones would ever hurt Rachel. “No,” she said. Had he ever hit her or “touched any of your private parts or anything?” Again Becky said no. The detective asked if both Gray and Jones had stayed home on Sunday. Becky said her mom had slept all day, but Jones had gone to a friend’s house and to the store. Did any of the kids go with him? “Rachel,” Becky said.

“Just her and him?” the detective asked. Yes, Becky said.

Barry Jones’s home at the Desert Vista Trailer Park in Tucson, Ariz.

Back at the hospital, Pesqueira and Gray sat outside in Pesqueira’s police car. There were no rooms available inside, Pesqueira would later explain. Relatives voiced concern that Gray had not been read her rights, but Pesqueira reassured her. “You’re not in custody, and I’m talking to you as a mom, OK?” she said. “I just wanna know what happened to your baby.”

Gray repeatedly told Pesqueira that she could not picture Jones hurting Rachel. The night before, Rachel had asked if she could sleep in the middle of the bed “’cause she wanted to sleep by Barry too.” It sounded stupid now, Gray said, but Jones made her feel safe. When her ex used to get drunk and beat her up, other men would never intervene. But Jones protected her. “And nobody’s ever done that.”

Gray recalled a couple of days when Rachel seemed to be afraid of Jones. And Rachel had recently come home with a black eye, which Becky blamed on Jones, saying he’d hit Rachel with a rake. But Rachel said it wasn’t true. Gray explained that Becky, who was going through a “lying phase,” sometimes got jealous and picked on her little sister. Gray discovered she had been using Jones to scare Rachel, threatening that if Rachel told on Becky about anything, Jones would hurt her.

Gray said she did not know how Rachel had gotten so many bruises on her body. “Angela, did you cause any of these injuries?” Pesqueira asked. Gray said no. Then Pesqueira told her that Ruelas had found no record of Jones taking Rachel to the fire station. “Oh no,” Gray said.

Outside the Choice Market where the 8-year-old Lopez twins claimed to see a man hitting a little girl. No records exist showing detectives visited the store.

The interrogation of Barry Jones is hard to watch.

At 10:11 a.m., Pima County Sheriff’s Detective Michael O’Connor leads him into a small interview room. Jones is short, just 5 foot 7, and disheveled. He is wearing a red T-shirt and jeans that hang loosely from his hips. His long, scraggly hair is thinning on the top. The detective who brought him from the transient camp had found him passed out, later describing him as distraught and “extremely wobbly.”

“I don’t know if anyone’s told you yet, do you know why you’re down here?” O’Connor begins. “No,” Jones answers. “I took the little girl to the hospital and her mom this morning,” he says. “I need to see my old lady to the baby.”

Then O’Connor tells him that Rachel is dead.

What! No.

I’m not lying, Barry.

No.

I’m sorry.

She gonna be all right. No. (starts crying) No. No. No. No. No. No. No. She’s all right. She’s all right. No. No. No. No. God.

Jones says he wants to go see Rachel. O’Connor says that Rachel has wounds that are “consistent with, um, uh, an abused child.” Jones screams.

Now, Barry …

No, no, no, no, no.

Barry, please listen to me. I don’t know what happened, OK. Or how these things may have happened to this child, OK. I do know …

She’s only 4.

Jones sobs and buries his head in his hands. O’Connor asks him to compose himself and then reads him his Miranda rights. While O’Connor briefly leaves to get a box of tissues, Jones remains slumped over the table, moaning.

Pima County sheriff’s officers would later describe suspicions about Jones’s hysterics. “I felt he was acting,” Sgt. Michael Downing said at a pretrial hearing. “He started to slam his head against the table. I thought it was a joke.”

When he spoke, Jones answered questions in sobbing, guttural bursts. At times he seemed dazed, offering rambling memories of Rachel: how he sang her a lullaby but did not know all the words; how he built a bed for her — and she “was all proud, proud of that little Rachel bed. Boy, made me feel so good, you know. She liked her little Rachel bed.”

Over the first two hours in the interrogation room, O’Connor was able to elicit some basic information from Jones. Much of it matched Gray’s general account. Jones said he had napped on and off on Sunday and at one point saw Rachel fall out of the van, where she had been playing with two little boys. “And she said one of ’em pushed her out,” he said. She didn’t cry, but she had a knot on her head. He gave her half a Tylenol or an aspirin and she went back out to play. Later Rachel went with him to get some frozen burritos for dinner at the Choice Market nearby. “She carried the milk for me,” he said.

Sometime after that, Jones said, neighbors noticed that Rachel looked sick. After laying her down for a short nap, he noticed there was blood on her pillow, which scared him. He loaded her into his van and headed toward the Rural Metro Fire Station. But there was a police officer there, Jones said — and his driver’s license was suspended. He drove on to the Quik Mart down the street, where he saw an EMT. The man shined a light in Rachel’s eyes. “He said something about her, her eyes being reactive equal, reacting equal, something,” Jones said. The EMT told him to keep ice on Rachel’s head, and “that’s what I done.”

Jones said he had noticed the bruises on Rachel’s stomach when Gray put her in pajamas the night before. O’Connor asked about Rachel’s other bruises. “What other bruises?” Jones asked. There were bruises that appeared to have been healing for weeks, O’Connor said. “I don’t know,” Jones said. “Her mama told me she bruised real easy.” Gray had not wanted to take Rachel to the hospital, Jones said. “She just said last night, I’d take her to the emergency room, but they’d take her away from me.”

O’Connor asked Jones if he had ever spanked Rachel. “Never,” he said. Jones admitted yelling at the kids — he sometimes called Rachel a “whiny butt” and sent her to her room — but he didn’t believe in physical punishment. “It don’t serve no purpose.”

Nearly three hours into the interrogation, Pesqueira arrived. Things soon escalated. She told him that Becky had accused him of hitting Rachel. She also implied that Brandie had made accusations, too. “Did you know that your own daughter has said certain things about what you did to her?” Pesqueira asked.

I did to who?

Did to Rachel.

No. I never done nothing to Rachel.

Did you know that you could be facing first-degree murder charges? First-degree murder, Barry, that’s what we’re talking about.

Me?

You. You. Because everything points to you, Barry.

Jones swore he did not hurt Rachel. But “I let her die,” he cried over and over again. Detectives insisted he was lying. Pesqueira called him a “piece of shit.” Downing suggested Jones had lost his temper. “She pissed you off, didn’t she?” he asked. “Rachel was a good girl,” Jones cried.

At one point, Downing said Rachel was looking down from heaven unable to rest, asking Jesus why Jones would not admit what he did. “She would never lie to Jesus,” Jones said.

After almost five hours, the interrogation ended. Jones was put in handcuffs and booked for first-degree murder and child abuse.

A front-page story in the Arizona Daily Star the day after the arrest of Barry Jones.

In a front-page story on May 3, 1994, the Arizona Daily Star reported on the arrest of Barry Jones. It mentioned Rachel’s alleged fall from the van, but also quoted an anonymous neighbor who described how Rachel had walked into her camper trying to vomit. “Her face was a greenish color, then it turned white,” she said. Jones “looked real concerned for her.”

An autopsy was conducted that same day. Dr. John D. Howard, a pathologist with the Pima County Medical Examiner’s Office, conducted the procedure while Pesqueira watched.

There were signs Rachel was not well cared for. She was underweight, just 28 pounds. Her baby teeth showed decay. The external injuries included “blunt genitalia trauma” and a deep cut on her scalp. But the head injury was not what killed Rachel. Instead, Howard found “an irregular laceration of the descending portion of the duodenum” — part of Rachel’s small intestine. It was a relatively rare injury, commonly associated with car accidents, and likely caused by a sharp blow to her stomach. “Death was caused by small bowel laceration due to blunt abdominal trauma,” Howard wrote in his autopsy report.

Meanwhile, Pima County detectives kept interviewing children. A woman named Norma Lopez had contacted the sheriff’s department, saying that on May 1, around 4 p.m., her 8-year-old twins — a brother and sister — came home from the Choice Market near the Desert Vista. They said they had seen a man with “flying hair” hitting a little girl while driving a van. The girl was crying — “They could hear her and they could see it,” Lopez told the detective. When she saw the news about Jones’s arrest on TV, “I knew right away the kids saw the same guy.”

Interviewing young children can be fraught with risk. An unqualified questioner can extract unreliable or imagined recollections. At the time of Rachel’s death, coercive or suggestive interviewing of children had led to a rash of lurid, elaborate, and false accusations about ritual sexual abuse at daycare centers across the country. The resulting wrongful convictions are still being overturned.

Despite the existing research in 1994 recommending best practices for interviewing children, the Pima County Sheriff’s Department had no such protocols in place. The twins were interviewed in each other’s company, with their mother present. Both said they saw a man hitting and elbowing a little girl while driving a van. When Laura, the sister, said she had not watched the 5 o’clock news to confirm that Jones was the man she saw, Lopez reminded her that she had. The detective asked Laura if she really remembered watching the news. “A little,” she said. When Ray, the brother, couldn’t estimate the age of the man in the van, Lopez brought up her own brother, who was in his 30s. “OK, was he about like your uncle?” the detective asked. “Uh huh,” the boy said.

The Lopez twins would become key witnesses for the state.

Becky, too, would become an important witness against Jones. After her mother was arrested on May 3, she and her 14-year-old brother, Jonathan, were taken in by their aunt Donna Foster. The next day, Foster contacted detectives, saying Becky had something new to share. In a videotaped interview, Becky recalled overhearing Rachel telling her mother that “Barry hit her with a metal shoe bar in the head.” Becky didn’t see the shoe bar, or really know what a shoe bar was. But she heard her mom and Jones arguing about it. “Becky states she was present when Rachel told their mother that Barry had caused the injuries to her,” the detective wrote in a report.

While detectives collected statements against Jones, signs began to surface that Gray abused her kids. When Foster picked up Becky and Jonathan from school after their mother’s arrest, she found them unkempt and wearing clothes they had outgrown, according to an affidavit she later provided to Jones’s federal defense attorneys. The kids ate voraciously, awed by the amount of food she had at her home. Before long, Foster called Child Protective Services with concerns that Becky had suffered abuse and “possible inappropriate sexual touching,” according to a subsequent medical report. Becky told doctors that her mother hit her in “all sorts of places,” including her stomach and face.

Angela Gray’s own upbringing was marked by trauma. According to Foster’s affidavit, Gray’s 18-year-old mother killed herself when Gray was young; her father moved her from Massachusetts to Arizona, only to give her up for adoption. By the time she was a teenager, Gray was doing drugs and living on the streets, Foster said. Gray’s sister had told police at the hospital that Gray seemed depressed and ill-equipped to raise her kids.

The consequences were particularly dire when it came to Jonathan, who was born deaf. Gray did not provide the care he needed to learn to communicate; when he was little, Foster remembered Jonathan “screaming at us because he could not speak.” It was not until he was 12 years old that he was enrolled at the Arizona School for the Deaf and Blind, where administrators found “he could only read at a second-grade level,” according to Foster.

During Jonathan’s own interview with Detective Ruelas on the day Rachel died, he seemed confused, asking if his sister was going to stay in the hospital. He had gone to school that morning. No one had told him what was going on. Through an interpreter, Jonathan referred to Jones as his “friend,” saying at one point he had pulled Rachel’s hair, but “not hard.” Jonathan said Jones never spanked Rachel, just sent her to her room.

Jonathan would never take the stand. Nor was the evidence of Gray’s abuse admitted at Jones’s trial. Jurors never heard about it.

The Rural Metro Fire Station where Barry Jones told Angela Gray he sought medical assistance for her daughter.

Upon arriving at the Pima County Jail, Jones wished aloud he could trade places with Rachel. He was put on suicide watch. Shortly afterward, Jones received notice of his indictment and the state’s plan to seek the death penalty. He also received a letter from Gray.

“Angela baby, if I could tell you what happened to Rachel I would in a minute and we would not be where we are,” Jones wrote back. He told her what happened after he left her at the hospital. First, he had picked up the kids and taken them to his twin brother Larry’s house. Then he asked a friend to go with him to see a man named Ron, who lived in a school bus at a nearby transient camp. He planned to return to the hospital, but Ron told him he was having a “breakdown” and gave him a pill to calm him down. Jones passed out. The next thing he knew, he was being arrested.

“Babe I lied about the fire station,” Jones wrote. He explained that he’d seen a sheriff’s officer and wanted to avoid him since he had no license or plates. He apologized, “but Rachel’s head was bleeding and Fire Station and Paramedic sound much more comforting to a mother than Quik Mart and EMT.” The thought that someone hurt Rachel made him feel sick, he wrote. “It makes me think I should have hung around the house more often and not been gone so much.”

Meanwhile, a private investigator named George Barnett began working on the case, hired by Jones’s court-appointed attorneys. An Air Force veteran who did three tours in Vietnam, Barnett had worked as a Tucson police officer until opening his own practice. In mid-May, he visited the Desert Vista Trailer Park.

Barnett recorded his findings in a 16-page report. He heard the same thing again and again: Jones was not known for physical violence and neighbors trusted him with kids. A manager of the trailer park said he was quiet and polite, and seemed to have a good relationship with his daughter, Brandie. One woman said Jones would often help his neighbors with repairs, asking only compensation for the parts. If he lost his temper, he just walked away — and “his payback would be in the form of never assisting or helping that person who made him angry,” Barnett wrote.

But Angela Gray was another story. Several people told Barnett she yelled at her children when Jones was not around. One neighbor said that she had stopped letting her daughters play at Jones’s home after Gray moved in. She believed Jones wasn’t really in love with Gray but tolerated her because he didn’t want to kick her out with her children. “I can’t believe that Barry had anything to do with harming that child,” the neighbor told Barnett.

Not everyone had described Jones in glowing terms. The day after his arrest, his ex-wife, Carol, told detectives that during their marriage, he had been “angry most of the time.” He was out of work and using drugs, lashing out and cursing at the kids. He had not generally been violent, she said, but in that period “he took a belt to ’em” a few times. When she decided to leave him, he threatened to kill himself in front of the kids and was forced into psychiatric treatment. But a former manager at the trailer park told Barnett that Jones had quit drinking and “was much less agitated” than he had been during his marriage to Carol.

Leann Jones, who was married to Larry, said Jones was far from perfect, but he would never hurt a child. “I mean, there’s things Barry probably has done over the years that he should be in jail for, but not for that,” she told me. The brothers were born in South Carolina and grew up in a volatile household, moving constantly. Their mother, herself a victim of abuse, drank heavily, beat the kids, and once stabbed her husband, according to interviews with family members conducted by Jones’s federal defense team. Jones began stealing and was sent to Vision Quest, a program for delinquent youth. By the time he shacked up with Gray at the Desert Vista, they were both hooked on crystal meth.

Barnett also learned that Jones had been having an affair with a woman named Rose, the friend who went with him to the transient camp the day Rachel died. Rose was his ex-girlfriend; her own daughter, Elishia, remained close to Jones. On the phone, Rose told Barnett that Jones had shown up distraught that morning, saying that Rachel was in a coma and convinced it was because of the head injury.

Barnett’s report was filled with leads to pursue. The co-owner of the Desert Vista told him he had heard that a “2-year-old boy who was slightly large for his age had struck Rachel in the stomach with either a stick or an iron bar.” After the arrests of Jones and Gray, the mother of the boy “packed her things and moved within two hours without notifying the office,” Barnett wrote. Neighbors said she was “scared to death” that her son might be responsible for Rachel’s injuries.

But just a week into his work, Barnett was told by Jones’s attorneys that continuing to pay him was “financially infeasible.” Barnett would stop his investigation until further notice. He never picked it up again.

Angela Gray on the day of her arrest at the Pima County Sheriff’s Department.

George Barnett died in 2014. But in a sworn affidavit signed in 2002, he said he was certain he could have proven Jones’s innocence had he been able to keep investigating. He had not even realized that Jones was represented by Sean Bruner, a Tucson defense lawyer who was the lead attorney on the case; Barnett had only ever met with his co-chair, Leslie Bowman. He was never called to testify at trial.

Bowman, who is now a U.S. magistrate judge, acknowledged in a 2002 affidavit that she failed to seek additional funds to pay Barnett. She had only practiced law for about a year, yet Bruner delegated major responsibilities in the capital case to her, such as interviewing all witnesses. She never even spoke to Gray.

Jones expressed confidence in his lawyers in his early letters from jail, which he wrote mainly to Rose and Elishia. He rarely mentioned Bruner but was upbeat about Bowman, who he called Miss Leslie. She was “pretty as a speckled puppy,” he wrote, and “sharp as a tack.” He observed that “Mr. Sean is piling on the work on her.”

But as time went on, Jones described lapses in communication with Bowman and concerns that the state was manipulating the evidence against him. “The really rough part is that I believe they already know of my innocence but do not want to look stupid so they try to fabricate a story against me,” he wrote.

Jones had been in jail for six months when he got word that his twin brother, Larry, had died. Jones sought permission to go to his funeral but was denied. He spiraled downward after that. As his trial approached in the spring of 1995, Jones sent a letter to Bowman. “Dear Miss Leslie,” he wrote, “wanted to write and see what is happening. It is getting close to trial time and I am becoming very scared.”

Defense attorney Leslie Bowman, left, in Pima County Superior Court on May 28, 2010, in Tucson, Ariz.

Amonth before the start of the trial, Brandie was deposed by attorneys for Jones, Gray, and the state. Brandie repeated that Rachel had been hit in the stomach by a little boy using an iron bar, but now claimed to have seen it herself. A defense attorney for Gray brought up a boy named “Ryan,” who Brandie had briefly mentioned during her interview with Detective Ruelas, while listing the kids who lived in the trailer park. Brandie said Rachel used to talk about a Ryan who was always being mean to her.

Brandie also said that Rachel’s older brother, Jonathan, used to sleep in the same room as the girls. When he entered the room, Rachel would say, “Can I sleep with you, Brandie?” A defense attorney asked if Jonathan ever tried to touch Brandie in a bad place. She said he did once, and she told Gray. After that, her dad built a separate room for Jonathan on the other end of the trailer.

In her 2002 affidavit, Bowman said she never attempted to contact Jonathan, “although he was both a potential suspect and a potential witness.” Years later, as part of Jones’s federal habeas appeal, attorneys collected sworn affidavits from several people at the Desert Vista who said that girls were afraid of Jonathan. Jones’s niece Tera said that both she and Brandie had experimented sexually with him, but she thought it was possible he’d molested his little sister since she believed he could not control himself.

In one affidavit, Elishia said Jonathan chased girls, touching their breasts or grabbing them between their legs. “He was very rough,” she said, “and he went after the little girls as well as those of us who were a little older.” A neighbor said that she had found her five-year-old daughter under a blanket with him. Elishia’s sister called Jonathan “the nastiest little pervert.” But she also said there were “lots of crazy, perverted people there.”

Indeed, the same affidavits are rife with allegations of sexual abuse by adults at the Desert Vista. One man named Bob was a known “molester” who was “always saying ‘hi’” to Rachel, Tera said. According to a 1993 report from the Pima County Sheriff’s Department, Brandie also accused a neighbor named Robert of fondling her at the trailer park. And Jones’s twin brother, Larry, had a bad reputation among the kids, mainly for being mean and violent — but also at one point for taking “inappropriate showers” with his stepdaughter Chelsea, Leann’s daughter.

Chelsea is in her 30s now. She remembers the Desert Vista as a place where the kids ran around barefoot and the adults all did crank. She has deep anger at Larry for being abusive. Yet she recently began writing to Jones in prison. “The one thing that’s always stood out to me is that he always tried to protect my mom,” Chelsea told me. When Jones saw Larry harm her mother or the kids, Chelsea said, the brothers would end up in a fistfight.

Today, Chelsea wonders if Larry should not have been an alternate suspect, along with so many others at the Desert Vista. As Tera said in her affidavit, Rachel was not shy. “She would go with almost anyone. Since Angela was always sleeping off her highs, Rachel was unsupervised a lot.”

Photo of Rachel Gray.

The trial of Barry Jones began in April 1995. Angela Gray had recently been acquitted of murder, with her attorney pinning Rachel’s death on Jones. She was convicted of child abuse and given eight years in prison.

Superior Court Judge James Carruth presided over both trials. Sean Bruner, Jones’s defense lawyer, told me Carruth had a reputation for being a bit lazy and going along with the state. “He liked to move things along real quickly,” he said, an observation supported by the trial transcripts. While Bruner said this hardly set Carruth apart from other judges, another veteran Tucson defense attorney, Richard Lougee, was scathing. He told me Carruth had once spent a major trial doing his taxes and reading Golf magazine. “His attitude toward justice was aggressive indifference.”

Representing the state was Kathy Mayer, head of the Pima County Attorney’s Special Victims Unit. A longtime prosecutor and advocate for gay rights, Mayer was tough. She had navigated homophobic attacks from city council members in the ’80s and proved formidable in court. She also had a reputation for integrity. “I’ve never thought of her as one of the sleazy attorneys in that office,” Bruner said, calling her “terrific.” Lougee, who tried sex crimes cases against Mayer for decades, compared her favorably to other prosecutors of the era, while also describing her as an ideologue and “true believer.” “She tried people rather than facts,” he said. “She was very good at what she did. I had no reason to think she was dishonest in any way.” But “once she became committed to a case, she got tunnel vision.”

In her opening statement, Mayer described what caused Rachel’s death. She had died from a condition called peritonitis, which is caused by a rupture of the small intestine. As a result, fluids that are supposed to pass through the intestines “leak out into the rest of our body, and it slowly poisons us,” she told jurors. It was a painful death — and it was not an accident, Mayer said. “Who killed her? The state contends Barry Jones killed her.” They had eliminated “any other possible suspect.”

The trial lasted just over a week. The state sought to prove that on the afternoon of May 1, 1994, Jones had beaten and raped Rachel inside his van. To prove it, Mayer called witnesses who said that they saw Jones coming and going with Rachel. The time frame for each trip was shaky, based on loose estimates from kids and adults. “A lot of people in this case that aren’t good at telling time,” Mayer was forced to tell jurors by the end. But it all happened between 2 p.m. and 5:30 or 6 p.m.

Particularly important was Becky, Rachel’s sister, whose statements continued to evolve. At her mother’s trial just a few weeks earlier, where she had cried on the stand, Becky repeated what she had always said — that her sister had taken two trips with Jones and that she seemed OK when she came home. But testifying against Jones, Becky suddenly said there had been three trips. She also recalled seeing bruises on Rachel’s face and hands. She had never mentioned these before. Finally, she said Rachel acted scared of Jones, who sometimes hit her while they played. “Barry would want a hug and Rachel wouldn’t go there,” Becky testified.

The Lopez twins also took the stand. Both were asked to act out the part of the man with the messy hair hitting the little girl while driving the van outside the Choice Market. Ray Lopez said the girl was crying, but he could not see her face — and he did not recognize the van when shown a photo. His sister, Laura, said she saw the girl’s face “a little” and could see her eyes watering. But their mother, Norma, testified that her children were sure of what they had seen. “They came running in — they were out of breath and anxious to tell me the story,” she testified.

If anyone inside the Choice Market saw something suspicious that day, the state did not call them to testify. In fact, there is no hint in any of the police reports that anyone from the Pima County Sheriff’s Department ever visited the store. Yet the state did call an employee from the Quik Mart, where Jones had said an EMT had looked at Rachel. The employee said a man with a little girl had come in for some ice during her shift — but not at the time when EMTs from the fire station usually stopped by.

On April 12, 1995, Sonia Pesqueira took the stand. She had recently been promoted to sergeant. In Bruner’s opening statement, he said there was no physical evidence to show Jones had raped and killed Rachel. It was up to Pesqueira to prove the opposite.

No semen or pubic hairs had been found to show Rachel was raped. But a serologist had testified that there were trace amounts of blood (too little to effectively analyze) found on the shirt Jones was wearing the day of his arrest, along with small stains on his jeans. The latter matched Rachel’s blood type. Small amounts of blood had also been found on and around the passenger seat of the van, some of which also matched Rachel. With Pesqueira on the stand, Mayer would use the blood evidence to show that Jones had beaten Rachel during the third trip in the van, then raped her behind her seat, leaving an “impression stain” on the carpet.

Pesqueira readily admitted that she was not an expert in bloodstain interpretation. But she had once attended a weeklong workshop on the topic in Scottsdale, Arizona. Asked by Mayer to help the jury understand the “terms [of] art that you use to differentiate maybe one type of stain or spatter from another,” Pesqueira said that bloodstains could be matched to different velocities, for example. “Because I am not qualified as an expert to say what velocity they are, I could say I could appreciate what type of stains they were in relationship to where the victim could have been and the assailant could have been,” she said.

It was confusing. It was also well outside the bounds of Pesqueira’s expertise. At one point, Bruner objected. Carruth said her claims sounded “awfully speculative to me.” But he let her proceed. Pesqueira walked the jury through the photos to show how, when Jones struck Rachel in the passenger’s seat, blood from her head would “spatter out.”

Pesqueira also analyzed photos of Rachel’s bruises, sorting newer ones from older ones based on their color and appearance. Another photo showed that Rachel had “linear contusions on her lower abdomen below her rib cage.” These were “consistent with pattern injuries,” in which a tool or instrument leaves an impression on human skin, she said. Mayer asked if Pesqueira found an item that was consistent with the pattern in the photograph. “Yes, I did,” Pesqueira said. A pry bar was discovered under the van’s driver’s seat.

Jurors found the forensic evidence compelling. Hildegard Stoecker remembers the blood in the van and on Jones’s clothes as “the main thing” she found convincing. “But you can read that two different ways,” she said. “Now I look back at it and realize, well, that could’ve been just simply from him carrying her and her being in the van — it doesn’t necessarily mean that he killed her.”

Bruner did not call any expert witnesses to challenge Pesqueira’s testimony. Nor did anyone explain the unreliability of eyewitness accounts from children, or the pitfalls of assessing injuries based on observation alone. Finally, and most crucially, there was no expert witness who could counter the state’s theory about the timing of Rachel’s fatal injury.

Instead, Bruner called just one witness for the defense: 12-year-old Brandie Jones. Since her father’s arrest, Brandie had moved from one relative’s house to another and attended four different schools. From the jury box, Stoecker felt sorry for her. She remembered seeing Brandie in the restroom before she testified, going through a trash bag filled with clothing given to her by a defense attorney. “She’s going through these clothes trying to figure out what to wear,” Stoecker said.

Brandie repeated the claim about the boy and the metal bar. Mayer easily cross-examined her, pointing out inconsistencies in her statements. Stoecker and others felt Brandie was just trying to help her dad. A juror named Odessa Poles remembers being disgusted at Jones and Bruner for putting the child in that position.

On April 14, 1995, Jones was found guilty. Bruner was not surprised. “It was a tough case,” he told me. The evidence had been weak, but “Barry’s the boyfriend, he’s a drug addict, you know, he kind of fit the stereotype, he lived in a really run-down part of town. It was kind of stacked against him, I guess you could say.”

If Bruner remains dispassionate about the conviction, it’s probably because he was always ambivalent about his client’s innocence. In an affidavit signed in 2002, Bruner said he could not explain why he did not do more to investigate the case. “In retrospect,” it reads, “it is possible I just assumed Mr. Jones was guilty based upon the state’s version of the case.”

There was another factor stacking the case against Jones. Jurors had been screened for their willingness to impose a death sentence, although their job was solely to determine whether Jones was guilty. Studies have long shown that “death qualified” juries are more likely to convict. In Jones’s case, this meant any jurors with lingering doubts could still vote for a guilty verdict, while psychologically distancing themselves from the implications. As Stoecker recalls, the possible death sentence loomed heavy over the jury. Yet Poles was shocked to hear that Jones ended up on death row. She believed in his guilt, she told me. But “I don’t feel that his lawyers fought hard enough for him or to really prove his case. … If I had had his lawyers, I’d rather have shot myself in the foot myself.”

Poles was deeply affected by the trial. It began on her granddaughter’s birthday, she repeatedly recalled. Years later, after leaving Arizona and falling into a depression, Poles realized she was still hanging on to the memory of the trial. “And my therapist tells me, ‘You’ve got to let it go,’” she said. “I can’t let it go.” It’s not that she’s gripped with hatred toward Jones. She just cannot get over what was done to Rachel Gray.

Poles and Stoecker both told me about encounters they had following the trial that assured them they did the right thing. Poles said she got on the elevator with Mayer, who told her that “certain evidence was withheld from us that we didn’t know about.” The implication was that it further proved Jones’s guilt. “But she never did tell us what it was.”

Stoecker had a much stranger story. Days after the trial ended, she said, she ran into someone from the prosecutor’s office in the checkout lane while buying groceries. Stoecker said it was a woman — she thought it was a prosecutor — but could not recall who exactly. Regardless, “she recognized me,” Stoecker said, and mentioned evidence against Jones that had not been presented at trial. “But the evidence was that [Rachel] did regain consciousness” at the hospital, she said, and that before she died, “she claimed he basically assaulted her.”

The claim made no sense. The emergency room doctor estimated that Rachel died hours before she arrived at the hospital. Nor was there any reason such evidence would not be admissible at trial. However irrational, it made Stoecker feel better, at least temporarily.

Over email, Mayer declined to discuss the case. But she wrote, “I would never have told a juror or anyone else that Rachel had regained consciousness at the hospital,” she wrote, “so that conversation did not happen with me.”

Correctional Officer Tracy Sisson works the command post at the Special Management Unit II high-security prison complex in Florence, Ariz., on Feb. 11, 1999.

The road from Tucson to Florence, Arizona, takes you out of the shadow of the Santa Catalina Mountains north to Highway 79. Two lanes lined with saguaros become Pinal Parkway, and soon, the Arizona State Prison Complex is impossible to miss. A long perimeter fence runs right alongside the road; at the intersection is the Blue Mist Motel, where relatives of death row prisoners sometimes stay the night before an execution. A trailer park houses workers across from the sprawling complex. In some ways, it resembles the Desert Vista.

Florence’s claim to fame is as the ultimate prison town. There are nine penitentiaries within a roughly 1-mile radius, both public and private. Each new prison project has brought promises of economic stability, but the local benefits are hard to discern. On a hot Saturday afternoon in September, the storefronts on Main Street were shuttered or empty. At the one open store — a cluttered thrift shop — pamphlets advertised jobs with the Arizona Department of Corrections.

At the Pinal County Historical Society and Museum, a glass display features nooses used for hangings, alongside black and white photos of the condemned. Beneath it, there’s the double execution chair used in 1934 to kill two brothers simultaneously in the gas chamber. Since Jones has been on death row, 33 people have been executed in the state, all but one using lethal injection.

The entrance to the Arizona State Prison Complex in Florence, Ariz.

In 1997, the year the Arizona Supreme Court upheld Jones’s conviction, he and others on death row were moved to Special Management Unit II, a new, high-tech experiment in punishment and isolation. The Tucson Weekly described how prisoners were “divorced from natural light except for the three hours a week spent alone in a narrow, concrete recreation pen.” Men were soon suffering psychological breakdowns. For Jones, who had a history of depression, the conditions would drive him close to suicide.

Others choose to hasten death with the help of the state. In 2000, Arizona killed Donald Miller, a “volunteer” who gave up his federal appeals. Among the witnesses to his execution was Sonia Pesqueira. She had investigated the murder that sent Miller to die. In a 2001 MSNBC documentary, Pesqueira expressed contempt toward his decision to “quit,” saying it was proof of his character.

Another witness featured in the film was a young, skinny defense investigator named Andrew Sowards. After the execution, he gave up murder cases for a while. But in 2008, Sowards went to work with the Arizona Federal Public Defender’s Office, arriving just as Jones’s federal habeas petition had been denied. As he traced the investigation to its origins, Sowards became increasingly convinced that Pesqueira — the same cop who had spoken so coldly about his old client — had helped send an innocent man to die.

In 2009, Sowards got access to the county attorney’s file in Jones’s case. “They claim to have an open file policy, and I wanted to go take a look,” he told me. The first box he opened contained a bunch of tapes. At the top was one that nobody in his office had ever seen. “It had never been disclosed, we didn’t have a copy of it in our file, we had never heard of it,” he said.

The tape featured a 1995 interview between a Pima County sheriff’s investigator and two young brothers. “Do you remember me, from seeing me before?” the investigator asked the older boy. She asked about an old injury on his chest. “Ryan, my brother, he took a piece of stick and sliced me,” the boy answered. He said it happened when his family was living somewhere else.

Sowards realized something was wrong. Ryan was the same child rumored to have hit Rachel with a metal bar, the boy whose mother abruptly abandoned the trailer park after Rachel’s death. His own parents had described him as a bully — and he was the same size as Rachel, despite being half her age. The tape certainly did not prove that the child was responsible for her death. But had it been disclosed to the defense before trial, as prosecutors were obligated to do, the tape would have provided critical corroborating evidence for Brandie’s testimony, possibly generating reasonable doubt among jurors. Instead, the state concealed the fact that they ever investigated the alternative scenario. In her closing statement to jurors, Mayer mocked the story about “the little boy who killed her with this sort of accidental thing with the metal stick.”

Sowards began obsessively pouring over the evidence. He tracked down a woman who had lived at the Desert Vista and briefly appeared in a report by Detective George Ruelas. She told Sowards that police had “grilled” her two young sons back in 1994, asking whether either of them hurt Rachel. But, like the interview with Ryan’s brother, this was not documented in the case file.

When Sowards sought to speak to Ruelas, he found him in a federal prison, convicted in a drug heist committed while working as a California Highway Patrol officer. Sowards wrote him a letter. He asked about several gaps in the investigation, including whether he or anyone else ever visited the Choice Market. Ruelas never replied.

Other critical pieces of evidence had long been missing. Among them were the blue panties that Rachel had been wearing when she was brought to Kino Hospital. Sowards was told by Pesqueira that they were most likely destroyed. But eventually, a portion of the underwear was found and tested for DNA, with no match to Jones or anyone else.

Litigation over the missing evidence and DNA testing led to a delay that would prove crucial for Jones. In 2012, the U.S. Supreme Court decided Martinez v. Ryan. Until the ruling, onerous procedural barriers governing cases like Jones’s dictated that, if attorneys failed to bring a claim of ineffective assistance during state post-conviction proceedings, that claim was forever barred from being heard in federal court. But Martinez carved out an exception, holding that if such a claim was itself the result of ineffective lawyering by post-conviction counsel, a defendant could have a new shot at relief.

A paralegal with the Federal Public Defender’s Office had reviewed the billing records from Jones’s post-conviction attorney. Several key files were not mentioned. The records suggested the attorney did not even read the full case, let alone thoroughly investigate it. In 2014, the 9th Circuit Court of Appeals remanded Jones’s case to a federal district judge, who reopened the door to federal court. As Jones’s current attorney, Assistant Federal Public Defender Cary Sandman, explains, “If his case had actually proceeded more rapidly through the system, in theory, he might have faced an execution before 2012 and had been dead already.”

But for all the missing evidence and holes in the investigation, perhaps the most important discovery made by Jones’s legal team were key changes in the testimony of Dr. John Howard, the medical examiner who was a state witness against both Gray and Jones. Just weeks apart, Howard gave conflicting accounts about the timing of the injury that killed Rachel. At Gray’s trial, Howard estimated that both the vaginal injury and the fatal intestinal wound were “most consistent” with occurring 24 hours or more before Rachel died. But when he took the stand against Jones, Howard testified to a shorter time frame, concluding that the injuries were consistent with being inflicted 12 hours before Rachel’s estimated time of death — precisely the window offered by the state for Jones’s trips in the van with her.

The failure to confront Howard is one mistake Bruner readily admits. He had attended Gray’s trial, he just did not pick up on the discrepancy. “I could have cross-examined him on that 24-hour/12-hour thing, and I missed that,” Bruner told me. “It’s an important case, I should have caught that, and I didn’t.”

In 2004, Howard provided Jones’s previous federal appellate attorneys with an affidavit explaining his testimony. “When I testify, I answer only the questions that are asked,” he said. If trial attorneys had asked whether Rachel’s fatal abdominal injury could have happened “more than 24 hours before her death, I would have answered the question in the affirmative.” Howard was unaware that Rachel had been described as looking sick as early as Saturday, April 30, two days before she was brought to the hospital. Her symptoms would be “consistent with the abdominal injury being inflicted prior to that time,” Howard said.

A slew of additional experts has since dismantled the medical evidence heard by jurors. Dr. Janice Ophoven, a renowned pediatric forensic pathologist who first reviewed the tissue slides and other evidence from Rachel’s autopsy in 2002, has long insisted that her intestinal injury “could not possibly have been inflicted on the day prior to her death.” She emphasized that “the veracity of this evidence is as scientifically precise as any forensic determination in medical science.” Dr. Mary Pat McKay, who first studied the same materials in 2009, says there is “absolutely zero evidence” that Rachel’s fatal injury occurred within 24 hours of death. And in an affidavit signed earlier this year, Dr. Phillip Keen — who was initially contacted by Leslie Bowman in 1994 to review the autopsy report, but never called to testify — said he agrees with Ophoven and McKay: “Rachel’s small bowel laceration was not inflicted on May 1, 1994, and thus Jones’s jury was misled to believe otherwise.”

Kathy Mayer speaks to students during a workshop titled “With Conviction: Science in the Courtroom” at the University of Arizona in Tucson on Sept. 26, 2015.

In 2009, the same year Sowards found the tape hidden in the Jones file, the National Academy of Sciences released a landmark report raising questions about the reliability of a wide range of forensic practices. Of particular concern were disciplines based on “pattern matching,” which rely primarily on visual observation. The report singled out bloodstain interpretation as one such field, relying on analysis that is “more subjective than scientific.”

There was never much doubt that Sonia Pesqueira had testified outside of her expertise at Jones’s trial. The NAS report cast further doubt on her analysis. But in fact, it was worse than that. On the stand, Pesqueira said her training in bloodstain analysis had been taught by a woman named Judith Bunker, who held workshops for “law enforcement agencies and detectives worldwide.” This was true — Bunker was once lauded as a pioneer in blood interpretation; in 1980, the Fort Lauderdale News marveled at the “44-year-old grandma who is the only blood spatter analyst in Florida.” But while Bunker’s pupils went on to testify at trials, capital defense attorneys would find that she had grossly exaggerated her credentials, claiming to have years of technical experience in an era when she was working as a secretary to a medical examiner.

Over email, Bunker said she is retired and proud of her work. “I will stand on my background and training,” she wrote. “My qualifications were accepted in many courts throughout the country in bloodstain pattern analysis and reconstruction.” She added, “I cannot speak to what a former student does after they left my class.”

It is no surprise that Bunker was allowed to testify in courtrooms nationwide. Although judges are the “gatekeepers” who vet expert witnesses, most do not have the background to easily determine what is sound science and what is not. The same is true of lawyers, on both sides. In Arizona, high-profile exonerations like that of Ray Krone, sent to death row on bogus bite-mark evidence, have forced prosecutors to admit that flawed forensic evidence can send innocent people to prison.

In 2014, Pima County launched a Conviction Integrity Unit, tasked with investigating claims of actual innocence. Veteran prosecutor Rick Unklesbay was put in charge. The next year, Unklesbay joined Jones prosecutor Kathy Mayer, along with Krone himself, on a panel to discuss wrongful convictions. Mayer blamed the abuse of forensic evidence on “professionals acting unprofessionally.” Unklesbay stressed the need for prosecutors to police themselves. After all, when an innocent person is sent to prison, Unklesbay said, the real perpetrator “is free to offend again.”

A recent photo of 54-year-old Barry Jones was shown by his attorney Sylvia Lett.

The Pima County CIU had yet to exonerate anyone in June 2017 when Cary Sandman sent a letter to Unklesbay. It included a lengthy summary of the problems in Jones’s case, including the opinions of medical experts debunking the state’s timeline for Rachel’s fatal injury. Sandman explained that, pending the outcome of Jones’s upcoming evidentiary hearing, he had been told by the Arizona Attorney General’s Office that Unklesbay would be involved in any potential settlement of the case. He offered to meet and provide “any additional information you may request.”

In response, Unklesbay referred Sandman to the CIU’s website. The application guidelines were clear, he wrote: “The unit does not evaluate cases that are still proceeding on any form of appeal.” To Sandman, the reply was preposterous. In capital cases, habeas appeals don’t end “until the needle is inserted,” he said. “His response basically says to me that they’ll never look at a case that’s in litigation — and in a death penalty case, that means their office is just a sham.”

Over email, Unklesbay said he would “for obvious reasons” review a death penalty case involving an innocence claim. He said he did not remember his correspondence with Sandman. “If Jones should lose, the CIU can get involved,” he wrote.

A spokesperson for the Arizona attorney general declined to comment on the upcoming hearing for Jones. In its previous letter to Sandman saying the Pima County medical examiner did not dispute the findings of defense experts, the office said it did not plan to call a medical expert of its own. Yet the spokesperson told me it would be “completely inaccurate” to suggest that the original theory of the crime is no longer supportable. Arizona appears ready to defend its conviction of Jones. But it is not clear how.

In early August, Sandman deposed Sonia Pesqueira. She had recently retired, with a collection of awards and press coverage chronicling her decadeslong crusade for the state’s most vulnerable victims.

Sandman showed Pesqueira the statements from former Pima County Medical Examiner John Howard suggesting Rachel’s fatal injury occurred at least 24 hours before Rachel died. “This is all new to me,” she said. Pesqueira had never consulted him on the timing of Rachel’s injury. If she had known it had possibly been inflicted before Sunday, May 1, 1994, she said, she would have widened her investigation. Sandman brought up other holes in the investigation. For example, he asked what happened to the clothes Rachel wore on the day she was supposedly raped and beaten. They would potentially have significant forensic value. But there was no record they were ever collected. Pesqueira could not answer why.

When I first contacted Pesqueira for an interview in late August, she quickly agreed. “Although this case was 23 years ago, the images of what I saw are still vivid in my mind,” she wrote over email. But when I arrived in Tucson in September, she wrote that she had been taking care of her sick grandchildren and had come down with a fever herself.

A few days later, I stopped by her house in a pleasant neighborhood on Tucson’s east side. The entrance had a striking view of the Catalina Mountains and a sign reading “Bienvenidos.” There was nobody home. After I left her a note, Pesqueira sent a text message saying she was at the doctor’s office but could speak very briefly “because I will be busy after today.”

Pesqueira stood by her investigation. She speculated that the peritonitis could have taken effect faster in Rachel than in other children. She was 4 years old but “itty bitty,” no heavier than her own 2-year-old grandson, Pesqueira recalled. She denied any rush to judgment and maintained her belief that Jones is guilty. “He probably doesn’t want to accept the reality of it, that he did what he did,” she told me.

The East Lawn Palms Mortuary in Tucson, Ariz., where Rachel Gray is buried.

A short drive from Pesqueira’s home, the East Lawn Palms Mortuary is dotted with bright fake flowers, spaced in neat rows. Under a tree in an area called the Garden of Love, a stone marker reads “Rachel Yvonne Gray, 1990-1994,” carved with a shepherd and lambs. There are no flowers on the grave.

Angela Gray got out of prison in 2003. She declined to be interviewed. Years ago, in a letter to Jones’s post-conviction lawyer, Gray said she felt “the jury gave him justice for the victim.” But today, she no longer believes Jones killed or assaulted her daughter.

In a 2009 affidavit taken by Jones’s defense attorneys, Gray said she only ever suspected him because of his lie about going to the Rural Metro and the fact that he did not return to the hospital that morning in 1994. She said Rachel called Jones her “Best Buddy Barry,” and always wanted to tag along with him. Finally, Gray reiterated something she had always insisted: that some of the bruises seen on Rachel’s body at the hospital and during the autopsy had not been there on the night of May 1, 1994. “The morning that I found Rachel, I was freaking out,” Gray said. Carrying her from her bed to the van, “it is possible that I hit parts of her body against objects in the house.”

Jones has not spoken to Gray since going to death row. As his hearing nears, he is cautiously hopeful about the possibility of freedom. He is also “scared to death,” he said. “That’s not my world out there,” he told me in a brief phone call from prison. “This is my world in here.”

Jones said it bothers him that while everyone has been focused on his appeals for years, nobody seemed to remember Rachel, or the fact that her killer is still out there. “It’s been all about me,” he said. In his letters from jail, Jones used to describe visions of Rachel visiting him, either in dreams or hallucinations. He wondered if others were haunted by her death.

“I mean, she didn’t get to live a life, you know? That’s the thing … I couldn’t tell you much about her except she was just a sweet kid. She was crazy about going to the store. She wanted to drive up to the store every time we went up to Quik Mart. She wanted to be around the other kids. She wanted to play. … And right now, she’d be like 26, 27 years old, you know, and have a family of her own and everything, you know? And these are things that I think about, that I can’t quit thinking about, that maybe nobody else thinks about.”

Top photo: The van driven by Barry Lee Jones, where he was accused of raping and killing 4-year-old Rachel Gray in Tucson, Ariz.