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Former FBI agent Robert Fitzpatrick has long cast himself as a whistle-blower who urged superiors to drop James “Whitey” Bulger as an informant in the 1980s, only to be ignored as corrupt agents protected the murderous gangster.

It’s a portrayal he offered while testifying for the families of Bulger’s victims in wrongful death suits against the government, during court hearings delving into FBI corruption, in a book about his life, and as a defense witness at Bulger’s 2013 racketeering trial.

In a stunning development Thursday in the never-ending Bulger saga, the 75-year-old Fitzpatrick was recast as a villain as prosecutors unsealed a 12-count indictment accusing him of perjury and obstruction of justice while misleading jurors in an effort to bolster Bulger’s defense.

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The indictment alleges that since 1998, Fitzpatrick, who was second in command of the FBI’s Boston office in the 1980s, “falsely held himself out as a whistle-blower who tried to end the FBI’s relationship with Bulger.” He’s accused of lying in an effort to aid Bulger’s defense, and misstating his accomplishments as an agent to enhance his credibility.

The indictment also alleges Fitzpatrick lied when he said he had found the rifle used to kill the Rev. Martin Luther King Jr. on the day he was assassinated in 1968, and when he said he had arrested then-New England Mafia underboss Gennaro “Jerry” Angiulo in 1983.

Fitzpatrick, of Charlestown, R.I., was led into federal court in Boston in shackles Thursday. He pleaded not guilty to the charges, was released on a $50,000 unsecured bond, and declined to comment as he left the courthouse with his wife.

His attorney, Robert Goldstein, said, “Mr. Fitzpatrick adamantly maintains his innocence, and looks forward to challenging the government’s allegations in a courtroom as soon as possible.”

The indictment shocked some relatives of Bulger’s victims who had sat through the eight-week trial that culminated with his conviction for participating in 11 murders while running a sprawling criminal enterprise from the 1970s to the 1990s. Bulger is serving two consecutive life sentences at a federal penitentiary in Florida.

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“I can’t believe it,” said Patricia Donahue, whose husband was killed by Bulger in 1982. “Everybody thought he was the one doing the right thing, and he ends up being indicted.”

Donahue said she believes Fitzpatrick should be held accountable if he lied, but questioned the timing of the charges now, and wondered why other FBI agents have eluded charges despite allegations that they took payoffs from Bulger, leaked information that got people killed, and provided explosives to the gangster.

“It seems to me they only pick certain agents to go after,” she said.

Fitzpatrick is the third former FBI agent to face charges related to Bulger. John J. Connolly Jr. was convicted of federal racketeering in Boston, and of murder in Florida. H. Paul Rico was indicted for allegedly assisting Bulger in the 1981 murder of Tulsa businessman Roger Wheeler, but died before the case went to trial.

Connolly’s FBI supervisor, John Morris, who pocketed bribes from Bulger and leaked information to him, was granted immunity from prosecution in exchange for his cooperation.

Assistant US Attorney Fred Wyshak, part of the team that prosecuted Bulger, said Thursday, “Much of the misconduct that has occurred as a result of the FBI’s relationship with James Bulger was not prosecutable due to the . . . statutes of limitations.”

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As for Fitzpatrick’s indictment, Wyshak said the allegations against him “occurred in 2013 in federal court, and were clearly prosecutable within the statute of limitations.”

Bulger’s lawyer, Hank Brennan, who is appealing his client’s conviction, called Fitzpatrick’s indictment shameful, and said he believes the former agent is being targeted for having the audacity to challenge the version of facts presented by the government.

“It doesn’t matter if a witness lies, steals, or murders, if you are a soldier of the federal government they will wrap their arms around you and embrace you,” he said. “If you defy them, they will crush you.”

Brennan said he believes Fitzpatrick was truthful, and his indictment will send a chilling message to anyone who testifies against the government.

He noted former governor William Weld testified in 1998 that while he was the US attorney in Boston, Fitzpatrick told him he feared for the safety of Brian Halloran, who was cooperating against Bulger and was denied placement in the government’s witness protection program. Later, Halloran and Michael Donahue, who was giving him a ride home, were gunned down by Bulger.

Fitzpatrick was called to the witness stand by Bulger’s defense lawyers to describe corruption in the FBI, and to try to undermine evidence that Bulger had been an FBI informant.

The defense contended that Bulger was never an informant, and that Connolly fabricated his informant file to cover up their corrupt relationship.

Fitzpatrick said he was sent to meet Bulger in 1981 to assess whether he should remain an informant, and Bulger told him he was not an informant, that he paid others for information.

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The indictment alleges that Fitzpatrick’s account of the conversation was a lie, and that he lied about advocating to drop Bulger as an informant.

He’s also accused of lying in testifying that he had been assigned to the FBI’s Boston office in 1980 to stop leaks that compromised investigations; the indictment states it was a routine transfer, with no special role.

Assistant US Attorney Zachary Hafer said in court that the six perjury counts carry a five-year maximum sentence; the six obstruction counts have a maximum term of 10 years.

Fitzpatrick, who coauthored a book, “Betrayal, Whitey Bulger and the FBI Agent Who Fought to Bring Him Down,” faced withering cross-examination during Bulger’s 2013 trial.

Former Massachusetts State Police colonel Thomas Foley, who had spearheaded the Bulger investigation in the 1990s, said Fitzpatrick failed to do anything to stop Bulger when he had the chance, and his testimony “was making a mockery of the whole process.”


Shelley Murphy can be reached at shmurphy@globe.com. Follow her on Twitter @shelleymurph.