by Joe Sexton, ProPublica, and Nate Schweber, Sep. 18, 2014, 6:33 p.m.

For more about the disappearance of 6-year-old Etan Patz, a case that frustrated and mystified police for decades, read the story ProPublica produced with WNYC in 2013.

Earlier this week, prosecutors played a confession given by the man they have charged with the 1979 murder of Etan Patz. In it, the accused, a former bodega worker from the Patz family's Manhattan neighborhood, is calm and composed in detailing how he strangled the 6-year-old boy and disposed of his body in a box. Pedro Hernandez cups his head in his hand at one point, crosses his legs casually in another. He chuckles at a prosecutor's joke. The prosecutor, seated across a table, carefully advises Hernandez of his rights and questions him methodically.

On Thursday, a very different version of the confession was played in Manhattan Supreme Court. This confession had been taken in a New Jersey police precinct after Hernandez had been questioned for more than seven hours by detectives excited about solving one of America's most famous missing child cases.

In this version, Hernandez sobs. Detectives, in a cramped corner of an interrogation room, rub Hernandez's head and gently touch his shoulders. The detectives invoke Hernandez's faith as an encouragement for him to come clean. The environment is highly charged.

"That's strength," one of the detectives says as Hernandez starts to detail his account. "That's the strength of the Lord."

At another point, detectives place a missing person poster with Etan's face on it before Hernandez.

"What did you do to him," a detective asks.

"I choked him," Hernandez says.

The detectives then ask Hernandez to write down in a notebook what he had just said.

"How do you spell choke," he asks.

"C-H-O-K," the detective instructs. "Sign here."

The fate of Etan Patz has nagged achingly at New Yorkers for decades. The boy had been on his way to school alone when he vanished. A manhunt was undertaken. National headlines followed. The FBI joined New York police in the investigation.

But the case had never been solved. Suspects were identified, and one was even found culpable for Etan's death in a civil proceeding. But the boy's body was never found. No one was ever criminally prosecuted.

The prosecution of Hernandez, still in its infancy more than two years after his arrest in May of 2012, is the latest uncertain chapter in the Patz saga. The arrest came with declarations of triumph by police and prosecutors, but also with skepticism among many, including FBI agents who had long worked on the case.

The playing of the two confessions arose as part of a judicial hearing to determine whether either would be admissible at a trial.

Prosecutors have sought to depict the raw emotions of Hernandez seen in Thursday's version as evidence of his authentic guilt. The tears, for them, are genuine, a logical and natural consequence of a painful, shameful unburdening. The appeals to his faith were an effort to get at the truth of what happened.

For Hernandez's lawyer, the behavior of the detectives is manipulative, and the anguish of his client is the consequence of what can happen when a mentally ill man is interrogated out of public view for hours.

In court on Monday, the lawyer, Harvey Fishbein, said all versions of Hernandez's confession are provably wrong when compared against the known evidence about the crime. But Fishbein said he does not doubt that Hernandez, a man with an IQ of 70 and a long history of treatment with anti-psychotic medications, believed what he was telling detectives.

The idea that people could falsely confess to serious crimes and provide compelling details of the rapes or killings they did not commit has been a subject of growing concern in the judicial system. Some states and localities have taken steps to try and limit false confessions.

One of those steps has been to re-examine police interrogation techniques. Another has been to require the taping of initial interrogations. New Jersey, it turns out, is one of the state's that demands recordings. But that's not what happened when Hernandez was questioned in New Jersey in May of 2012.

Prosecutors have argued that taping the seven hours Hernandez spent being interrogated by detectives was not required because it was a New York case, not a New Jersey matter. And they have said they were not obligated to advise Hernandez of his rights because he was not formally in custody. Fishbein has disputed that, saying that Hernandez more than once said he wanted to go home, but was instead kept in the interrogation room. Fishbein argues that all of Hernandez's ensuing confessions should be thrown out because of the failure to read Hernandez his rights during the hours of untaped questioning.

The confession played Thursday, then, captures a kind of middle stage in Hernandez's 36 hours with the authorities -- after the untaped interrogation, but before the more decorous interview in the offices of Manhattan prosecutors.

The detectives often make physical contact with Hernandez. They touch him, nearly hug him. They applaud his eventual admissions.

"You did the right thing today," one detective says. "It takes a lot."

Another detective asks if Hernandez wants to say anything to the Paz family.

"That I'm really sorry, that I never meant to hurt their child," he says. "That I hope they can forgive me."

Near the end of the recording, Hernandez remarks to a detective that he knew that what he had said would get a lot of attention.

"Because this is a big case," Hernandez says.