BOSTON — Ailing ex-FBI agent John “Zip” Connolly is waging a final battle to clear his name in a bombshell allegation that prosecutors withheld mobster James “Whitey” Bulger’s prison manuscripts.

Connolly was convicted of second-degree murder in 2008, largely based on the testimony of Bulger hitmen Stephen Flemmi and John Martorano — who admitted “to a combined 43 murders,” according to a motion for Post Conviction Relief filed in Florida Monday.

Connolly was found guilty of the murder of World Jai-Alai President John Callahan, who was shot in the back of the head and left in the trunk of a car in Miami International Airport in July of 1982. Martorano, who has long been a free man, did the killing. The Florida Commission on Offender Review voted 2-1 to grant Connolly a medical release from jail in 2021 to treat his cancer in Massachusetts.

Connolly has long fought that conviction and with Monday’s motion, filed by Boston lawyer Peter Mullane, he also accuses both Miami-Dade and Boston prosecutors of withholding knowledge of a handwritten manuscript by Bulger.

Mullane adds in the motion that because Connolly was at Harvard University studying for a master’s degree, a fellow agent said his client was “walled-off” and could not have warned Bulger and his crew that Callahan was a risk due to his knowledge of another World Jai-Alai murder.

“My client spent 19 years in prison and shouldn’t have spent 19 minutes,” said Mullane, “but it has taken a lifetime to just clear his name.”

Connolly is 83 and on home confinement in Lynnfield, but his lawyer told the Herald he’s “not willing to give up. He wants to clear his name for his wife and three grown children, too.”

In the motion, Mullane accuses a former Florida prosecutor of “persistent misconduct” — including “granting favors to witnesses, coordinating witness testimony, and sidelining unreliable witnesses.” That Miami-Dade assistant state attorney, Michael Von Zamft, resigned in 2024.

Mullane also states that another FBI agent, John Morris, had the “necessary motive, means, and opportunity to have leaked information to James Bulger, which resulted in the murder of John Callahan.” Morris, the motion adds, was given immunity for testifying against Connolly.

Robert Fitzpatrick, former Assistant Special Agent in Charge of the FBI’s Boston Office, is also named in the motion as the one who stated Connolly was “walled-off” from the case. Fitzpatrick pleaded guilty to 12 counts of an indictment charging him with perjury and obstruction of justice in connection with his testimony at the 2013 trial of James “Whitey” Bulger.

Mullane said Bulger was a “top-echelon informant” for the Department of Justice at the time and his client was just doing his job to rid Boston of the mafia. Yet, Bulger and his Winter Hill Gang was still operating in the streets of the city.

Connolly was convicted of second-degree murder for wearing his FBI-issued sidearm when he met with Bulger in Boston to warn him of what businessman John Callahan knew. Bulger was murdered in a West Virginia prison in 2018.

Mullane said it was common FBI practice to wear a department-issued sidearm at all times.

But it’s Bulger’s own writings that Mullane is hanging this new appeal on, writing in the motion that: “In his statements to the FBI and in his manuscript, Bulger asserted that John Connolly had been framed, revealing that his source inside the FBI’s Boston Office was actually John Morris.”

Connolly has long been named as Bulger’s handler, but this motion alleges the Boston office of the FBI at the time was using the mobster as an informant.

Bulger’s “concealed manuscripts,” coupled with the Miami-Dade prosecutor’s resignation, show a “pattern of wrongdoing that prejudiced Mr. Connolly,” the motion states.

Mullane states that fellow FBI agent Morris framed Connolly over the Harvard master’s degree nod — Zip landed the coveted seat, Morris did not.

“This was the source of Morris’s hatred for Connolly,” Mullane writes, adding that Bulger considered Morris “my guy” — not Connolly.

Mullane is calling for Connolly’s conviction and sentence to be vacated or, be granted a new hearing on the “suppressed” evidence — “along with any additional relief the Court deems just and proper.”

He lashed out at judges for allowing prosecutors to bend ethical boundaries to win convictions and he writes that the Boston FBI and DOJ were equally morally corrupt.

Martorano has long been a free man; Flemmi is either in prison or in a witness protection program.

“The prosecution can’t use psychopaths. That’s what happened,” said Mullane. “The system can use this as an example and stop people from getting convicted.”

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