John “Zip” Connolly, the ex-FBI agent convicted over his ties to slain Southie mobster James “Whitey” Bulger, has lost his bid to clear his name.

The 3rd District Court of Appeals in Florida denied Connolly’s bid for “postconviction relief” from his second-degree murder conviction. But, as the Herald first reported, he remains free from jail while on a medical release.

Still, his Boston lawyer Peter Mullane said Thursday, the aging former G-man wants to resurrect his reputation.

“The decision is moot in a street sense, but not moot for John who wants to clear his name,” Mullane told the Herald. “He’s totally and completely innocent.”

Connolly argued in a motion that “Florida, violated his due process rights by failing to disclose” witness testimony that he says would have cleared him.

He added he was hired by the FBI in 1968 “tasked with cultivating certain government informants, including James J. “Whitey” Bulger and Stephen “the Rifleman” Flemmi, two notorious members of a rival criminal organization, the Winter Hill Gang.”

Connolly’s target, he adds, was “to infiltrate the La Cosa Nostra, an organized crime syndicate responsible for a myriad of murders in the Boston area.”

The only problem was Bulger and Flemmi were equal-opportunity killers in the city.

Yet Mullane writes in his motion — and again in an interview with the Herald — that Connolly’s case did not include key testimony from former assistant agent-in-charge of the Boston FBI office, Robert Fitzpatrick.

The motion states: “Fitzpatrick attested he informed (a colleague) that Connolly was sequestered from the (incriminating) investigation because, during that time, he was pursuing a graduate degree at Harvard University.” Fitzpatrick also offered up another potential suspect.

The Florida appeals court did not bite. His conviction was “affirmed.”

Mullane said the judges in Florida were swayed by public opinion and the media coverage didn’t help. The movies and books on Bulger’s brutal history and life on the lam didn’t help either.

As for Connolly, who is in his 80s, he’s convalescing at home in Massachusetts “dealing with medical issues and trying to stay alive,” Mullane added.

Connolly was convicted in 2008 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.

Callahan, the former president of World Jai Alai, was shot dead by John Martorano, one of Bulger’s hitmen. Martorano testified he was working for Bulger when he killed Callahan, who was also a friend of his. Bulger wanted Callahan dead because the Boston businessman could implicate them in a 1981 slaying of another World Jai Alai executive.

The Florida Commission on Offender Review voted 2-1 in February of 2021 to spring Connolly on a medical release because he had about a year to live after being called “terminally ill.”

The Herald has filed a public records request with the Florida commission seeking the minutes and audio of Connolly’s hearing that took place last week.

Another Florida judge, the motion adds, has stated the evidence in this shocking case was “overwhelming.”