On a stifling afternoon in the summer of 1996, Rodney Roberts pleaded guilty to a kidnapping. He had never met the victim, let alone held her against her will. Yet this is what he told the judge in the cramped Essex County, New Jersey, courtroom. His court-appointed defender had convinced him his only other choice was life in prison.

The state, Roberts was told, had overwhelming evidence that he had raped a teenager. Plead guilty to the lesser charge of kidnapping, he remembers his public defender saying through the bars of the court’s packed holding cell, and the charge of aggravated sexual assault will be dropped.

Roberts thought about the jury that had found him guilty—in the same courthouse—of sexual assault and sent him to prison ten years earlier. If he pushed for a trial this time, he feared he would be sent away for decades. He felt trapped by the system, by his past.

“I knew I was innocent,” Roberts says today, “but I had to choose the lesser of two evils. It’s like you got to pick between Satan and Lucifer.”

Roberts’s case is far from unique. The year he pleaded guilty to a kidnapping he did not commit, 92 percent of convictions at the criminal court of Essex County rested on plea agreements, according to court data. By the time Roberts had spent 18 years behind bars, that number had risen to 98 percent, meaning that just 2 percent of defendants exercised their constitutional right to a trial by a jury of their peers.

Today, more than 2 million Americans are incarcerated following a plea agreement. Although the issue has not been widely studied, criminologists estimate that between 2 and 8 percent of convicted felons—from 40,000 to 160,000 people—are innocent of the crimes to which they pleaded guilty, according to federal judge Jed S. Rakoff.

Wrongful convictions like Roberts’s aren’t the only tragedy in such cases. His plea to a reduced charge of kidnapping closed a case of aggravated sexual assault, and police stopped searching for the perpetrator. That left the 17-year-old victim continuing to walk the same streets as her rapist.

The case began in the early morning hours of May 8, 1996. A teenager—­identified as S. A. in court documents—­was walking down a street in Newark toward her aunt’s house when she sensed she was being followed. As she continued along the edge of Fairmount Cemetery, a man put his hand over her mouth, grabbed her neck, and, she later told police, threatened to “blow her head off” if she screamed.

The man dragged her into an empty parking lot and raped her, said the teen. She described her attacker as a dark-skinned man, 170 pounds and 20 years old, wearing a black-and-red T-shirt, a black hat, and brown boots, according to the police report.

Seventeen days later, police arrested Roberts a few blocks away from the crime scene. At that time, Roberts, 29, worked part-time in a law office and also as a salesman.

A street-racing enthusiast, he and a friend recently had gone in on a second­hand yellow-and-black Kawa­saki. They soon argued over who owned the bike. Tensions rose. A police car pulled up in front of the two men. (“I’m actually the one who called the police,” Roberts says today.) The officer asked the pair for their names and walked back to his patrol vehicle. When he returned, his tone had changed.

“Put your hands behind your back! You’re being arrested,” Roberts remembers the officer shouting at him.

“I knew I was innocent,” Roberts says, “but I had to choose the lesser of two evils.”

Roberts was handcuffed and pushed into the squad car. At the police station, an officer said he was being detained for a parole violation. About a week later, Roberts was transferred to the county jail.

He was familiar with captivity. At 19, he had been convicted of aggravated sexual assault. That victim, a 32-year-old Newark woman, testified that Roberts was one of three men who stole her new car and raped her in January 1986. Today Roberts maintains he was the lookout, but a jury found him guilty. He got 20 years and was paroled after seven.

After he was released, Roberts moved in with his girlfriend and their son, Rodney Jr., born while his father was behind bars.

Starting a new life in New Jersey proved difficult. Roberts moved to North Carolina and found a job unloading trucks for a tire company on Fayetteville’s docks, which helped him build a small nest egg.

On his return to New Jersey a few months later, he found a paralegal position and worked at a menswear store on the side. But since leaving for North Carolina, Roberts had failed to report to his parole officer, a condition of his early release.

Now, under arrest, he knew he could be reincarcerated for the parole violation (the sentence would have been 20 months). But he hoped working two jobs and taking care of his son might be mitigating factors.

It was not until police took him to the Essex County Courthouse for arraignment that Roberts began to realize his predicament was far worse: A grand jury had indicted him not only for violating parole and stealing the motorcycle but also for sexually assaulting a teenage girl.

From his hallway holding cell, he told anyone who would listen that the police had arrested the wrong guy.

When the time came, Roberts refused to enter the courtroom, but from the hallway he could still hear the judge read the charges against him. He entered his plea from the hallway too: not guilty. Bail was set at $50,000.

A few weeks later, he was on the jail bus headed back to the Superior Court of New Jersey. A public defender, Charles Martone, introduced himself through the holding-cell bars.

Roberts asked Martone the basis for the sexual assault charge. Martone asked him what kind of plea deal he would accept. “I’m not taking a deal; I’m not guilty,” Roberts responded.

Martone returned 20 minutes later with bad news. He had just talked with the teenage rape victim. She knew Roberts from their Newark neighborhood, Roberts recalls Martone saying, and had identified him as her rapist in a photo lineup.

She’s inside the courtroom, Martone added, ready to testify against you. His attorney made Roberts’s choice clear: We work out a deal or you go to jail for the rest of your life.

Roberts remembered the stern faces of the jury when another judge read a guilty verdict back in 1986, convicting him of sexual assault at 19. He felt he had lost the presumption of innocence.

The Essex County public defender’s and prosecutor’s offices both declined to comment on Roberts’s case. But Georgia State University law professor Russell Covey, an expert on pleas, said this is a common quandary for past offenders.

“Prosecutors can induce those with criminal records to enter guilty pleas in cases where the evidence would not be strong enough to convince a first-time offender to give up his right to trial,” Covey said. As Roberts understood the deal being offered to him, the prosecutor would dismiss the sexual assault charge and downgrade the kidnapping charge.

“My attorney said the judge would put on the record that no one got hurt,” he says. “That was the part that made me consider pleading guilty to a crime I didn’t commit.”

The sentence, seven years in prison, was handed down by the judge on ­October 17, 1996.

After his plea deal and conviction, Roberts’s life changed overnight. The mother of his son broke up with him. His son began struggling with depression. Rodney Jr. says now, “I believed the whole point of him staying locked up was because he didn’t want to deal with me.”

A few months into his sentence, Roberts found something disturbing in his paperwork: The prison had classified him as a sex offender.

He started asking prisoners for advice. Word spread rapidly, and groups of inmates started calling him names, isolating him, and beating him up, as they did with others identified as child molesters. Roberts fought back. As a result, he estimates he spent more than 700 days in solitary confinement.

His first parole hearing came three and a half years into his term, in May 2000. He was brought into a room where two people sat on one side of a long table while a third observed him remotely, via videoconference.

When the parole board member on the small screen alluded to the sexual nature of his crime, Roberts answered that the judge had dismissed the sexual assault charge.

“I didn’t plead guilty to that,” ­Roberts remembers protesting.

“This is what we have to go by at this point,” replied another panelist, pushing a copy of the police report of the 1996 rape across the table toward Roberts.

Roberts would not admit to the crime or express remorse, both things parole boards listen for as they assess whether prison time has changed a person. His parole request was denied.

Back in his prison cell, Roberts felt as though he had been double-crossed by the justice system. He decided to take matters into his own hands. In January 2001, more than halfway through his seven-year sentence, he filed a motion to withdraw his guilty plea.

“I had no faith in public defenders at that point,” Roberts says. “I had to be my own lawyer.” Using the prison library’s IBM typewriter, he had copied the format of a model motion from a law textbook. Within a few days, the motion was denied.

Realizing he might have to serve the whole term, Roberts began spending most days at the library, studying for a paralegal degree from a distance-learning school and contesting his sex offender status.

In 2003, now at the end of his seven-year sentence, Roberts stood in the courtyard outside his cell with other inmates waiting to be released. When a warden called out a name, that prisoner stepped to the side and walked to freedom.

The choice was clear: Work out a deal or go to jail for the rest of your life.

Name after name was called. Finally, Roberts alone was left. He asked the guards sitting in the glass booth that controls the prison’s doors: “Did you forget me?”

He would not learn until the next day that the civil division of the attorney general’s office of Cumberland County, New Jersey, had lodged a detainer against him—a red flag suggesting he should not be released.

Instead, he was shackled and driven to a prison unit in Avenel, New Jersey, that housed criminals deemed too sexually dangerous to be free. A new, indefinite civil commitment was the price for his steadfastly refusing to admit remorse for a rape he didn’t commit.

After two years in Avenel—now nine years behind bars—Roberts got his first piece of genuinely good news. An investigator from the office of the public advocate named Ronald Price had unearthed a new lead: He had tracked down S. A., the rape victim, and interviewed her.

She had told him that she “did not even know anyone had been arrested for the crime” and denied ever having identified Roberts as her attacker from a mug shot or a lineup, according to the transcript of her interview.

Going through the case, Price also noticed the police report mentioned a rape kit. There was no record of what was found in it or of Roberts being asked to supply a DNA sample.

Once again, Roberts got to work. In 2006, he filed a petition with the Essex Vicinage Superior Court asking to withdraw his guilty plea to the kidnapping charge based on new ­evidence—or actually the lack of physical evi­dence tying him to the related rape that had landed him in a sex offender civil commitment program. Once again, the judge denied his motion.

It took two appeals and two more years of Roberts toiling away in the Avenel prison library for the court to agree to reassess the validity of his conviction “in the presence of all parties.” That meant that the victim and the man who had been convicted of charges related to her rape would face each other in court for the first time.

When that day came, in 2010, S. A. said she didn’t recognize Roberts.

“I want to know: Why did you confess to something that you didn’t do to me?” she asked him. The court’s rules prevented him from answering her.

The public defender who had represented Roberts in 1996 also testified. Charles Martone recalled the large backlog at the pretrial disposition court, but he didn’t remember anything about Roberts or his case.

“I was assigned to go through that backlog, offer plea offers that the state gave me to the individuals, advise them that this was the lowest plea offer,” he testified. “If they were guilty, they could decide to take it. If they were not, to take the case to a trial.”

His workload was overwhelming, he said, forcing him to divide his attention among up to 120 cases on any given day. But Martone said he never would have misled a client.

For the third time, Roberts appealed. The case was assigned to a new judge and finally to a new lawyer. In 2013, Roberts—now 17 years behind bars—met Michael Pastacaldi, a young private attorney who handles cases from the state on a contract basis. He wasn’t convinced of Roberts’s innocence.

“Why would someone plead guilty to something they didn’t do?” he remembers thinking. “It sounded like sour grapes.”

But the lawyer put aside his skepticism. He called the prosecutor’s office to ask whether a rape kit existed.

“He was the most persistent lawyer I ever had,” Roberts says.

On May 16, 2013, the Essex County prosecutor’s office ordered investigators to look for the missing rape kit. Just a month later, they hit pay dirt at the New Jersey State Police lab: the original kit, still sealed.

Three months later, Pastacaldi received a call from the prosecutor’s office: The tests were positive for semen, but it had never been tested for DNA. Pastacaldi filed a motion for DNA testing, and in September he got the call that would change everything. The DNA wasn’t Roberts’s.

On March 14, 2014, Roberts was finally freed. When he talks today about the police who arrested him, the public defenders who failed to prove his innocence, and the judges who kept him locked up for 18 years, no sign of resentment crosses his still-boyish face. Instead, to Roberts, the system that by design deprives the vast majority of defendants of their right to a trial—not its foot soldiers—is the guilty party. “Over the years, it started to become less and less about me,” he says.