NEW YORK — Thomas Donlon, a former federal agent who served as police commissioner last fall, sued New York Mayor Eric Adams and top current and former NYPD officials Wednesday, alleging they operated a “corrupt enterprise” that rewarded cronies and punished enemies at the expense of both the public and rank-and-file police officers, a copy of the suit shows.

Donlon, 71, who was brought in in September 2024 after Edward Caban resigned amid a federal investigation, alleges in the 251-page complaint filed in federal court in Manhattan that the department’s former top spokesman Tarik Sheppard threatened to “kill” him at the NYC Marathon after he discovered Sheppard had improperly used Donlon’s rubber signature stamp to approve Sheppard’s own promotion to three-star chief.

“I will f-----g kill you,” Sheppard allegedly said, according to the suit.

When Donlon demanded Sheppard face criminal charges, Adams did nothing except try to limit the public relations damage, the suit claims.

Donlon claims former Chief of Department Jeffrey Maddrey manipulated his daily schedule, planted “spies” in his office to keep track of what the new commissioner was doing and blocked attempts to initiate misconduct probes. Maddrey has since resigned under the cloud of a sex-for-overtime scandal.

The former commissioner claims Maddrey and Sheppard secretly switched out the names of officers he selected for promotion and replaced them with their own favorites while doctoring records to make it appear Donlon had signed off.

He also alleges that after a warehouse fire in 2022 destroyed decades of evidence and exposed sloppy practices, the NYPD promised to compile a comprehensive report on evidence storage. But, Donlon alleges, no report was done and when he toured warehouses in late 2024, he found the same sloppy practices.

And when Donlon’s wife got into a fender bender, the suit alleges, Sheppard leaked the details to the press to embarrass him.

Adams, Donlon alleges, either ignored his complaints or sided with Maddrey and his other loyalists – a major break from the past when mayors tended to back their police commissioners.

“This lawsuit is not a personal grievance; it is a statement against a corrupt system that betrays the public, silences truth, and punishes integrity,” Donlon said in a statement.

“The goal is to drive real change, hold the corrupt, deceitful, and abusively powerful accountable, and restore the voice of every honorable officer who has been silenced or denied justice.”

Adams’ spokeswoman Kayla Mamelak dismissed Donlon’s allegations as “baseless accusations from a disgruntled former employee who — when given the opportunity to lead the greatest police department in the world — proved himself to be ineffective.”

“This suit is nothing more than an attempt to seek compensation at the taxpayer’s expense after Mr. Donlon was rightfully removed from the role of interim police commissioner,” she added. “We will respond in court, where we are confident these absurd claims will be disproven.”

Adams appointed Donlon Sept. 13 after Caban hastily resigned following a visit from federal agents involved in the then-mushrooming corruption probe. On Nov. 20, Adams summarily dismissed Donlon in favor of Jessica Tisch. Donlon was shunted to a quiet role at City Hall before he was fired in April.

The lawsuit names Adams, Sheppard and seven other current and former top NYPD officials, including Maddrey, Chief of Department John Chell, First Deputy Commissioner Tania Kinsella, and now Deputy Mayor Kaz Daughtry.

The suit cites federal racketeering statutes in alleging the named defendants engaged in a criminal enterprise that included obstruction of justice, honest services fraud and retaliation against a whistleblower.

“The lawsuit asserts that Adams and his deputies weaponized the NYPD’s hierarchy to consolidate political control, shield sexual misconduct, and retaliate against anyone who challenged their authority,” Donlon’s lawyer John Scola said.

“Donlon’s refusal to play along made him a target — and the Department’s values, its officers, and the public all paid the price.”

Scola said the suit demands the creation of an independent federal monitor to oversee the NYPD’s system of promotions, assignments and discipline which Donlon claims are corrupted by politics.

It follows four lawsuits filed by top chiefs who similarly allege promotions were manipulated to benefit Adams’ NYPD cronies.

Republican mayoral hopeful Curtis Sliwa described the lawsuit as “terrifying but not unsurprising.”

“Under Eric Adams, the NYPD has become a disaster of pay for promotion, sex for perks, and a leadership culture that punishes integrity and rewards loyalty to the inner circle,” he said. “New Yorkers cannot trust a police department that operates more like a corrupt crew than a professional force.”

Spokespeople for the NYPD did not immediately reply to requests for comment.

Stepping in amid scandal

Donlon was running a consulting firm following a long career with the FBI when Caban stepped down after federal agents took his phone and those of several other high-ranking Adams appointees in the corruption probe.

But Donlon, the lawsuit states, was leery about the top police executives close to the mayor who might greet his appointment with “animosity and resentment.”

Indeed almost immediately, he claims, those executives began undermining him. After a cop was shot Sept. 14, Donlon ordered use of a single email chain to prevent wrong information from being conveyed to Adams. But Maddrey and Chell insisted, “We can speak with the mayor directly.”

When he moved to end misuse of social media by Chell and Daughtry by requiring them to clear posts with NYPD legal, they complained to Adams, the suit claims.

The mayor allegedly said, “Back off those guys, those are my best guys.” But on Jan. 28, Donlon’s concerns were validated when the city Department of Investigation issued a report finding the posts were “irresponsible and unprofessional.”

Donlon claims in the suit Maddrey diverted federal FEMA and counterterrorism funds to pay overtime to favored underlings — while Kinsella did little to monitor overtime spending. He alleges she told him, “They wouldn’t listen to me.”

While Donlon struggled to land a meeting with Adams, Maddrey had daily access.

Part of the undermining involved promotions and assignments. During two promotional cycles, Donlon’s picks were replaced without his knowledge with choices made by Maddrey and Sheppard and those were forwarded to City Hall, the lawsuit alleges.

“What resulted was a transfer of wealth in the millions of dollars at the hands of the defendants who falsified NYPD records to make it seem like Donlon had agreed to the promotional list,” the lawsuit alleges.

At another point, Donlon selected 10 cops for better assignments. But the transfers were rescinded by City Hall. The suit alleges Sheppard colluded with Deputy Mayor Camille Joseph-Verlack to block the transfers to embarrass Donlon.

In October, Donlon noticed Sheppard was wearing the three stars of an Assistant Chief. Sheppard had been a two-star chief a week earlier and Donlon hadn’t promoted him.

“To Donlon, this fraudulent promotion by Sheppard is “stolen valor” and is a crime,” the lawsuit alleges.

The dispute boiled over at the Marathon. Maddery intervened between the two men as Donlon’s daughter started to cry.

Donlon then ordered Maddrey to notify Internal Affairs. But Adams ordered the incident downplayed and Maddrey never ordered the investigation, the lawsuit alleges.

In a conference call, Adams told them to “patch up their differences.”

Donlon alleges accounts of the incident that were leaked by City Hall and Sheppard’s allies contained false details that distorted what happened.

“Under normal circumstances, Sheppard would have been fired,” the lawsuit claims.

After that Donlon knew his position was precarious, the lawsuit claims.

Donlon was then replaced by Tisch. According to the suit, Adams told him 10 minutes before announcing Tisch as the next police commissioner.

Donlon served out the remainder of his time with city government in the Deputy Mayor for Public Safety’s office.

His role was writing grants to aid the NYPD and the city’s other emergency agencies. But there was one more indignity.

On Dec. 16, Donlon’s wife Deirdre O’Connor-Donlon was rear-ended in traffic at East 56th Street and First Avenue on the East Side, the lawsuit states.

Two cops arrived and a sergeant. They determined O’Connor’s license was suspended. O’Connor had Donlon come to the scene with her insurance card.

All seemed fine and Donlon departed. The sergeant then got a mysterious call, and the dialogue took a turn.

O’Connor was handcuffed and taken to the 17th Precinct where she was placed in a holding cell for two hours.

She was finally given a summons and released. Fifteen minutes later, reporters began calling her phone.

The suit alleges Sheppard leaked the incident to the press, including the detail that the couple was living separately at the time.

In February, O’Connor filed a notice of intent to sue. In March, she called the 17th Precinct to get a copy of the summons, Donlon’s suit says. She was told it was “no longer in the system.”

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(Daily News staff writer Chris Sommerfeldt contributed to this story.)

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