Annie Dookhan quietly admitted she tampered with evidence and falsified documents that potentially affected tens of thousands of drug cases in Massachusetts before being led away in handcuffs to spend the next three to five years in the state women’s prison in Framingham.

Dookhan showed little emotion – except for a single tear that ran down her cheek as she sat in the witness box — as Suffolk Superior Court Judge Carol Ball queried her on her state of mind in changing her plea to guilty. Ball said she had a duty to ensure that the diminutive former chemist understood the rights she was giving up by admitting her guilt about six weeks before her trial was scheduled to begin.

“Are you pleading guilty here today because you are, in fact, guilty?” Ball asked.

“Yes, ma’am,” Dookhan replied, a phrase she repeated to about a dozen questions from Ball, with a couple “no, ma’am”s and her five “guilty” proclamations. Her only other comment was when the judge asked the correct pronunciation of her name, she said is it Doo-cahn instead of DOO-ken.

Dookhan was arrested and charged last year with 27 counts of perjury, intimidation of a witness by falsifying lab results, tampering with evidence, and lying about her credentials. An investigation by state officials and State Police determined Dookhan routinely altered or faked results by “dry-labbing” –estimating the type and weight of drugs by eye rather than actual lab testing – to help prosecutors gain convictions in drug trials. She faked results for several years, possibly as long as 10 years. So far, 649 inmates have been identified as warranting a review of their cases with 349 being released because Dookhan tested the drugs and testified in their cases, according to Department of Correction figures.

The scandal led to the forced resignations of Department of Public Health Commissioner John Auerbach and Health and Human Services Secretary JudyAnn Bigby, as well as the supervisor overseeing the Hinton state Laboratory in Jamaica Plain. The lab was closed and all testing moved to the State Police crime lab in Sudbury. All the Hinton chemists were placed on paid leave, with the last ones just returning to work a couple months ago. Dookhan was the only one charged, although the state Inspector General is looking at the processes and procedures at the drug lab to see if there was a systemic problem.

A CommonWealth story earlier this year found that there were piles of documents that showed Dookhan doing far more tests than the average chemist was able to do. Rather than questioning the results, the overworked colleagues complained that she was making them look bad. Dookhan’s lab supervisors gave her other assignments to try to slow down the number of cases she was allegedly clearing.

Despite Dookhan’s otherworldly production, often two and three times that of the average chemist at the Hinton lab, no one ever confronted or suspected her malfeasance until after her arrest. Dookhan was arrested when 90 vials of evidence disappeared from the lab without being signed out. Officials later discovered the initials of a coworker were entered on the records and Dookhan admitted she did it when confronted by State Police investigators.

David Meier, a former prosecutor who is now a private defense attorney, was brought in by the Patrick administration to gauge the scope of the scandal. Initially, officials estimated about 1,150 cases were tainted by Dookhan’s testing and testimony. That number was later revised to potentially as many as 34,000. In August, Meier released his report that said more than 40,000 criminal cases could have been tainted by Dookhan.

The American Civil Liberties Union and the state’s public defenders’ office are asking the Supreme Judicial Court to toss out all drug convictions that were tied to the Hinton lab – more than 190,000 – because the lax oversight and protocols at the lab could have resulted in other chemists doing the same thing as Dookhan.

Attorney General Martha Coakley said the “unique” case began and ended with Dookhan. “This case as it relates to Annie Dookhan is over,” Coakley said in an interview after the hearing. “We believe that this kind of behavior was limited to her. We believe this closes that chapter.”

Coakley said there is no indication anything was behind Dookhan’s actions other than an insecure worker trying to ingratiate herself with her superiors by being a productive worker. Dookhan had no prior criminal record.

“We haven’t seen something more nefarious,” Coakley said. “We looked to see if there were other motives or other incentives. She was diligent, she worked hard, people thought she was a good producer. But with her actions, she violated the whole integrity of the system.”

Assistant Attorney General Anne Kaczmarek recommended a 5- to 7-year sentence, higher than state guidelines of three years, because of the “egregious” damage Dookhan did to the criminal justice system as a whole. Dookhan’s lawyer, Nicolas Gordon, asked Ball for a one-year sentence. Ball took the middle ground and added two years probation after Dookhan is released.

“Someone in the system with her responsibilities knew or certainly should have known that by cutting the corners she went to the very heart of what the criminal justice system is,” said Coakley. “She violated that trust. There was a huge, huge impact on public safety. We felt it was really important, and I think the judge agreed in sentencing her to a term above the guidelines, that this sentence reflects that public officials have a very high bar, a very high standard to maintain.”

Pool photo by David L. Ryan/The Boston Globe