Annie Dookhan, a former chemist at the Hinton State Laboratory Institute, listens to the judge during her arraignment at Brockton Superior Court in Brockton, Massachusetts January 30, 2013. REUTERS/Jessica Rinaldi Want to know just how much our criminal justice system relies on plea-bargaining and how rarely prosecutions result in the kinds of jury trials we see on TV? Look no further than the story of Annie Dookhan, the disgraced Boston-area drug laboratory chemist whose egregious corner-cutting over a decade of work may have compromised more than 24,000 convictions in Massachusetts.

Dookhan had been working in a state lab operated by the Massachusetts State Police forensics unit and had personally tested thousands of drug samples used to convict defendants in criminal cases. Prosecutors were blindsided in 2012 when it turned out she had been routinely filing false test results and claiming to have detected the presence of drugs in samples she never actually examined. Dookhan was found to have been implausibly productive throughout her tenure at the drug lab, testing samples at a rate that was five times greater than that of her colleagues.

Dookhan pleaded guilty to obstruction of justice, perjury, and tampering with evidence in November 2013 and was released from prison this past April. But the ripple effects from a decade of malfeasance created a profound headache for the Massachusetts criminal justice system, sending lawyers throughout the state scrambling to determine which cases needed to be re-examined.

Last year, the Supreme Judicial Court of Massachusetts ruled that anyone who had pleaded guilty to drug charges based on test results prepared by Dookhan could take back their pleas. On Wednesday, the court followed up with a second ruling in a case involving a man who had been convicted at trial based partly on Dookhan’s discredited analysis. In an opinion, Chief Justice Ralph Gants wrote, “Regardless whether a defendant pleads guilty to a drug offense or is found guilty at trial, where Dookhan examined the substance in question as a primary or confirmatory chemist, the evidence is still potentially tainted by Dookhan's misconduct, the taint is still attributable to the government.” The ruling extended to defendants who had gone to trial the opportunity for a do-over that had already been offered to defendants who had pleaded out.

The court’s decision was applauded by the Massachusetts Bar Association, with chief legal counsel Martin Healy telling the Boston Globe, “We think that the level of misconduct and misrepresentation and fraud that occurred in the Annie Dookhan matter rises to the level of not being constitutionally sound. Anybody that’s convicted by a jury of their peers deserves to be either tried anew or the decision should be dismissed or vacated altogether.”

But it was the response from the Suffolk County District Attorney’s Office that was more illuminating, if only inadvertently so. In an email, D.A. office spokesman Jake Wark told the Globe that Wednesday’s ruling would only cause a “minimal disruption.” That’s because the vast majority of the roughly 7,500 Suffolk County convictions affected by Dookhan’s misconduct had resulted from plea bargains, not jury trials. (The ACLU of Massachusetts disputes Wark’s estimate of the number of Suffolk County convictions affected by Dookhan; a spokesman for the organization told me it is closer to 8,700.) In other words, the new ruling would not significantly expand the class of people affected by the bad tests because so few of those cases ever went to trial in the first place. Guilty pleas often lead to lesser sentences, making them enticing options. Flickr/Myfuture.com

It is a widely known but still underappreciated fact about the American legal system that criminal trials are extremely rare. When most of us imagine the gears of the justice system turning, we picture juries and judges listening to testimony and attorneys making dramatic courtroom statements in defense of their clients. But as Wark’s serene reaction to Wednesday’s ruling underscores, the reality is that almost all criminal cases are resolved through backroom deals between prosecutors and defense lawyers—a process that is poorly understood precisely because it happens outside of the public eye.

Why should we be concerned about the plea-bargaining system? Because, as U.S. District Judge Jed Rakoff has written in the New York Review of Books, the power to dictate the terms of a deal “is, as a practical matter, lodged largely in the prosecutor, with the defense counsel having little say and the judge even less.” Prosecutors run the show because, in most cases, the law gives them great flexibility to decide which charges to bring against a defendant and thus what kinds of sentences to threaten in order to pressure him into waiving his right to a trial. This is wrong not only because it is inherently coercive; it also leads to false confessions. Citing the National Registry of Exonerations, Rakoff noted in his NYRB piece that 10 percent of the 1,428 exonerations that were handed down between 1989 and 2014 involved cases in which a defendant had pleaded guilty.

Wark told me by phone that less than 5 percent of the 7,500 convictions the Suffolk County District Attorney’s Office has identified as being possibly tainted by Dookhan went to trial. “That’s simply the way things work in Boston, in Suffolk County, in Massachusetts, and in the United States,” Wark said. “The vast majority of every type of case is resolved through a guilty plea, and the reason for that is that the evidence is generally pretty strong.”

A defendant who wants a new trial based on Wednesday’s decision will now be able to file a motion to that effect, Wark said, and a judge will make a determination as to whether their case relied heavily enough on Dookhan’s work to warrant being retried. But Wark emphasized that prosecutors in Suffolk County don’t rely exclusively on lab results when they bring cases against drug offenders, and they typically bring a range of evidence that includes actual drugs and drug paraphernalia that have been seized.

“The sliver of cases that will be affected by this decision is a sliver of the already small number of cases that went to trial,” said Wark.