FRAMINGHAM — The Massachusetts State Police plan to fire 22 troopers and strip the pensions of another 14 recent retirees, as the state’s largest law enforcement agency seeks to bring to a close a yearslong overtime scandal that has sent a parade of troopers through federal court.

Massachusetts State Police Colonel Christopher Mason portrayed the punishment of the 36 troopers as a capstone to the agency’s own internal investigation into widespread payroll abuse. But more fallout looms. A US district court judge on Thursday reignited questions about the scandal and ordered prosecutors to re-examine whether it amounted to a broad criminal conspiracy.

In a news conference at police headquarters, Mason said the department will demand that the troopers reimburse taxpayers — dollar for dollar — for the pay they received for no-show shifts.

“These steps are necessary to send a message that there are consequences to conduct that is not aligned with the values of the department and with the integrity ingrained in the overwhelming majority of our members,” Mason said.

Forty-six troopers and higher-ranking officers have been implicated in a payroll fraud scheme that included phony tickets and falsified time sheets to cover for hours they never worked. Nine have pleaded guilty to embezzlement charges. One criminal case is pending.

Mason also announced Friday that prosecutors had reviewed cases for three dozen troopers involved in the scandal, but ultimately referred those cases back to State Police in May for administrative discipline. But US Attorney Andrew E. Lelling’s office disputed that characterization hours later.

“That is incorrect,” spokeswoman Christina Sterling said in an e-mail. “There have been no ‘referrals’ in either direction. This is an independent investigation by federal authorities."

The federal probe remains open, Sterling said. Lelling’s office also refuted a refrain that State Police leadership and Governor Charlie Baker have shared for months: that the criminal investigations into the high-profile fraud scandal began with a referral that State Police made to prosecutors.

State prosecutors also had a separate, parallel criminal probe into State Police payroll issues. Attorney General Maura Healey’s office announced Friday it was closing its probe and referring its investigative material to a division of the Inspector General’s office created in 2018 to provide oversight of State Police.

The 2,100-member State Police force has weathered a series of controversies in recent years, none more damaging than the overtime fraud scandal that emanated from Troop E, a now-defunct division that patrolled the Massachusetts Turnpike.

“I believe that there was a culture that was created at Troop E where supervision was lax, where supervision failed to address when officers would leave overtime blocks early or respond to them late," Mason said. "I think that that is something that will be an unfortunate part of the MSP history, something that we have to own, and something that I’m committed to ending that practice.”

State Police officials on Friday said the agency’s own internal probe of overtime abuse is now over, unless new evidence of misconduct surfaces.

The department said it will not investigate payroll or other records prior to 2015. In federal court this week, prosecutors revealed that records from those years contained damning evidence that showed at least one former trooper had collected more than double the amount of money that prosecutors believed he had stolen. Baker had previously pledged the department would review records going back as many years as problems were found.

State Police spokesman David Procopio said the “quality of record-keeping” was inconsistent and made it difficult for the department to look back further. He noted that the agency audited three full years of records and identified a pattern of abuse. “We believe we identified those who took part in that scheme,” he said.

Procopio refused to state the total amount in restitution being sought. He also declined to name the 36 troopers the department is seeking to fire or strip pension benefits from.

“Whether we do at the conclusion of the disciplinary process will be a decision the Department makes in light of interpretation of public records law related to personnel actions,” Procopio said.

This group of troopers — none of whom have been charged criminally — includes 13 active-duty members. Another nine have already been suspended without pay. Fourteen members retired in recent years, amid growing scrutiny.

The internal investigation into the overtime fraud scandal began three years ago and initially focused on just a single trooper before widening and sparking parallel criminal probes by state and federal prosecutors.

The criminal cases, in addition to restitution, have resulted in two troopers being sentenced to prison time, while six others were ordered to serve periods on supervised release. The state has moved to strip pensions from them. Those matters are pending before the state retirement board. Several did not have enough tenure to be pension-eligible.

Legal specialists have questioned the department’s record-keeping, transparency, and willingness to investigate itself. The department lost track of and destroyed some key documents.

Mason acknowledged the department’s record-keeping system “was less than adequate.”

"Clearly that is the case,” Mason said. He said records will now be “stored in a more responsible manner,” including to allow for a historical look back “in the event that we ever have an unfortunate event like this.”

Earlier this month, Baker and Mason announced policy changes and proposals to supplement a previous set of reforms launched in the spring of 2018, when they disbanded Troop E. Baker appointed Mason in November.

Friday night, Baker’s office released a statement saying it “supports all prosecutors’ offices’ continued efforts to hold accountable all those who broke the law.”

The efforts take aim at corruption and cultural problems that have plagued the force for years. They include increased supervisory oversight, enhanced ethics training, activation of GPS tracking technology in cruisers to monitor troopers’ whereabouts, and a proposal to allow state and municipal agencies to recover triple damages from police officers who knowingly submit false claims for hours worked.

Still, Mason said, “we still have a ways to go.”

“The public has a right to be skeptical with the Massachusetts State Police, and so we’re working hard to regain that trust,” Mason said.