Wearing a T-shirt that read “Free Bird,” an Arizona man who spent nearly 28 years on death row was freed on Thursday after a judge overturned his conviction on charges that he had sexually assaulted and murdered his girlfriend’s 4-year-old daughter.

Last year, the U.S. Supreme Court rejected a bid by the man, Barry Jones, for relief. But his lawyers entered mediation with prosecutors, who agreed this month that the conviction should be overturned and that he should plead guilty to a lesser charge.

Mr. Jones’s lawyers had argued that he had been wrongfully convicted because his trial lawyer was ineffective and failed to uncover medical evidence that he was not responsible for the injuries that caused the death of the girl, Rachel Gray.

At a hearing on Thursday, an Arizona Superior Court judge overturned Mr. Jones’s conviction on charges of child abuse, sexual assault and felony murder, and vacated his death sentence.

Under an agreement with prosecutors, Mr. Jones, 64, pleaded guilty to a lesser charge, second-degree murder, for failing to seek medical help for Rachel.

He was sentenced to 25 years — time he had already served during the nearly three decades he spent behind bars since his arrest on the day Rachel died, May 2, 1994.

Less than 90 minutes after the hearing, Mr. Jones was reunited with his family, including his three children, said his lawyer, Cary Sandman.

“It is an incredible feeling to be back in the arms of my family after 29 years,” Mr. Jones said in a statement on Friday. “I am so grateful to my defense team, who never gave up on exposing the truth in my case, and to my family, who stood by me throughout this terrible ordeal.”

Laura Conover, the Pima County attorney, whose office prosecuted Mr. Jones in 1995, said in an interview on Friday that her office had reviewed “voluminous expert transcripts” from a seven-day evidentiary hearing with medical experts that had been held in federal court in 2017.

“The idea that Mr. Jones had committed the fatal injury — the evidence was no longer there,” she concluded, adding, “The original theory of the state was flawed.”

“This is but one of myriad cases which highlight the frailties and the fallacies of the death penalty,” said Ms. Conover, who added that she opposes capital punishment. “This is why we should not be tinkering with the machinery of death.”

Ms. Conover noted the delicate balance in handling Mr. Jones’s case.

“I would acknowledge the road that he has been on,” she said. “Having been accused and convicted of an injury he seemingly did not commit has cost him dearly. At the same time, these are the heartbreaking cases we deal with when a 4-year-old suffers abuse and neglect.”

Rachel’s cause of death was determined to be homicide resulting from a small bowel laceration from blunt abdominal trauma, court records show.

Prosecutors argued that Mr. Jones had beaten and sexually assaulted her while she was under his care on May 1, 1994. He was convicted and sentenced to death in July 1995.

In October 2017, a federal judge held the evidentiary hearing with medical experts and investigators to examine Mr. Jones’s claim that he had ineffective representation at his trial.

The judge concluded in 2018 that Mr. Jones’s conviction should be overturned, finding that the police investigation was “colored by a rush to judgment and a lack of due diligence,” and that an effective lawyer would have brought these faults to the jury’s attention.

The trial lawyer failed to uncover “key medical evidence that Rachel’s injuries were not sustained on May 1, 1994,” the judge wrote, and failed to question other physical evidence and eyewitness testimony presented by prosecutors.

If the lawyer had properly defended Mr. Jones, “there is a reasonable probability that his jury would not have convicted him of any of the crimes,” the judge wrote. A federal appeals court panel later affirmed that finding.

But in May 2022, the Supreme Court ruled against Mr. Jones and another Arizona death row inmate, David Ramirez, in a decision that sharply limited prisoners’ ability to challenge their convictions in federal court by arguing that their lawyers had been ineffective in state court proceedings.

The 6-to-3 decision split along ideological lines.

Justice Clarence Thomas, writing for the majority, said that a federal court considering a habeas corpus petition, or a petition challenging the validity of a prisoner’s conviction or sentence, “may not conduct an evidentiary hearing or otherwise consider evidence beyond the state-court record based on ineffective assistance of state post-conviction counsel.”

In dissent, Justice Sonia Sotomayor wrote: “Two men whose trial attorneys did not provide even the bare minimum level of representation required by the Constitution may be executed because forces outside of their control prevented them from vindicating their constitutional right to counsel.”

Justice Thomas wrote that the “sprawling” evidentiary hearing in Mr. Jones’s case amounted to a “wholesale relitigation of Jones’s guilt” that was “plainly not” envisioned under a previous Supreme Court decision in 2012.

Justice Sotomayor responded that the hearing was required because Mr. Jones’s lawyers were ineffective.

“Far from constituting an inappropriate and ‘wholesale re-litigation of Jones’s guilt,’” she wrote, “the District Court’s hearing was wide-ranging precisely because the breakdown of the adversarial system in Jones’s case was so egregious.”

Mr. Sandman said he was grateful that the Arizona attorney general and the Pima County attorney had taken a fresh look at the case and had acknowledged that Mr. Jones “never received a fair trial.”

“We hope that Barry can enjoy the rest of his life in peace, surrounded by his family and friends,” Mr. Sandman said.

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