Earlier this year, the Justice Department appointed Robert Mueller to serve as special counsel to investigate connections between the Russian government and the campaign of Donald Trump. From both sides of the aisle came praise for Mueller, the former FBI director with an alabaster image.

The media was also nearly unanimous in its glowing coverage. Mostly ignored were Mueller’s role in the post-9/11 roundup of thousands of Muslims (subjected to arbitrary detention, beatings, humiliation), his botching of the anthrax investigation by ignoring a solid lead and fingering an innocent man (government legal settlement: $5.8 million), his silence as the Bush administration lied about Iraq as a pretext for war, and his his accommodation to Bush’s torture program (against protests by his own agents), which led one court to conclude that he and Attorney General John Ashcroft, “met regularly with a small group of government officials in Washington, D.C., and mapped out ways to exert maximum pressure on the individuals arrested in connection with the terrorism investigation.”

To the extent that anyone, in hailing his bona fides, paid attention to Mueller’s role in the notorious case of Boston criminal kingpin James “Whitey” Bulger, it was to describe Bulger’s arrest in 2011 as a masterful job of FBI investigation. In fact, the case of Whitey Bulger, a fugitive eluding capture for 16 years, had been one of the biggest scandals in the history of the FBI, and the Bureau’s official story of its resolution is so preposterous that it either casts a withering light on the competence of Mueller and his G men or reeks of something smellier in Mueller’s domain.

From 1979 to 1995, Whitey Bulger engaged in a criminal reign of terror that eventually established him as the most powerful underworld boss in New England. As so often in the annals of organized crime, the outlaw and the law were partners in a dread dance, and in late 1994, tipped off by his FBI handler, one John Connolly, that indictments were imminent, Bulger went on the lam and disappeared.

Beyond putting Bulger on the Ten Most Wanted list (and then not until 1999), the FBI went nowhere with the case for six years. After ascending to the Bureau’s leadership in 2001, Mueller likewise demonstrated indifference to apprehending Bulger until, a decade later and on the heels of his reappointment to the job, it was politically expedient both for himself and the U.S. government (of which more in a moment).

Questions about the FBI’s relationship with Bulger while he dominated Boston’s criminal underworld in the 1980s and ’90s have never been fully resolved. That a corrupt relationship existed is undisputed. From the 1970s Bulger had been a confidential informant of the FBI, recruited to help the Bureau take down the Italian Mafia. It was a toxic combination, through which Bulger only gained power.

To give but a taste of the dirty work: H. Paul Rico, who’d had a long, tainted career with the Bureau in Boston, was indicted for helping Bulger and an associate plan a murder in 1981 while Rico was head of security for World Jai Alai, a company Bulger was skimming. (Rico died in 2004 before he could be tried.)

John Connolly, Bulger’s handler beginning in the 1970s, is currently serving a lengthy prison sentence in Florida for the murder of a Bulger associate who was rumored to be cooperating with a criminal investigation.

Connolly’s supervisor, John Morris, has admitted to tipping off Bulger about another cooperating witness – information that Bulger used to murder this man, a mobster desperately seeking witness protection – and an innocent bystander in 1982. Morris, who got immunity for his cooperation, additionally admitted to receiving $7,000 in cash bribes from Bulger.

When Connolly alerted Bulger that he was about to be arrested, it was not the first time the agent acted to protect the crime boss. Connolly had thwarted previous investigations of the Boston PD and the Massachusetts State Police by telling Bulger of specific wiretaps and surveillance; as a result, those agencies had long been wary of cooperating with the Boston FBI.

By numerous accounts, Bulger and his partner in crime Stephen Flemmi, who eventually turned state’s evidence against Whitey, believed they were shielded from prosecution, if only because of the secrets they could spill. “If I’m going to jail, you’re going to jail,” Bulger once thundered to Morris, who soon after suffered a heart attack. Bulger’s defense lawyer has argued that a senior official in the U.S. Attorney’s office in Massachusetts, Jeremiah O’Sullivan, had offered Bulger immunity. O’Sullivan is dead and Connolly, who introduced the two, is disgraced, but the tangle of evidence suggesting systemic corruption or tacit accommodation has been richly documented in books and dramatized in film.

And where was the nation’s future top cop in the 1980s as Bulger and Flemmi routinely engaged in murder, extortion and drug trafficking, and as FBI agents waded in the gore? In what is doubtless an inconvenient coincidence for a man now characterized as a bloodhound for truth and justice, Robert Mueller was a criminal prosecutor in the Boston office of the Justice Department in the early ’80s and then acting U.S. Attorney for the District of Massachusetts in 1986-87.

It is possible that prosecutor Mueller, having earlier lost an infamous racketeering case against the Hells Angels in San Francisco, decided that securities fraud, New Cold War skullduggery and more mundane corruption better suited his ambitions. It is possible that FBI director Mueller, beset with the aftermath of the World Trade Center attack and his duties as an apparatchik in the Global War on Terror, had more pressing matters than Bulger.

But it’s at least as likely that Mueller was well aware from his time in Boston that the rot emanating from there went far beyond a few bad actors; that, as scandalous as the Bureau’s failure to capture Bulger was, it would be more scandalous still if Bulger had a chance to reveal the full extent of the rot; thus, the best way to protect ugly secrets about Mueller’s flailing agency and the Justice Department would be to let the crime boss run out his days in the shadows.

We may never know the reasons Mueller didn’t seem to give a rat’s ass for the Bulger investigation beyond the pro forma inquiry, when visiting the Boston Bureau as FBI director, “Where are we on Whitey Bulger?” And because Bulger, a high order rat, ultimately never did spill the secrets, preferring to hold to the fiction that he had never informed for the FBI, we still do not know the extent to which the government enabled racketeering and murder.

But if we don’t have answers, there are questions — not least of those being: how, once Mueller’s attentions were roused, did it take the Bureau a mere seven weeks to accomplish what had supposedly flummoxed it for 16 years? The official explanation for this amazing feat is absurd, involving, as we shall see in Part II, a PR agent inspired by the TV show “Alias,” photos of the crime boss that even the mother of his child couldn’t recognize, and a former Miss Iceland.

This part of the story begins in the aftermath of the U.S. government’s assassination of Bulger’s fellow mark on the Most Wanted list, Osama Bin Laden, in 2011. Much was being made of the fact that Bin Laden had lived so long untroubled in Pakistan, the implication being that Pakistani officials were wily Orientals and all-around friends of terror who also probably hated America for our freedoms.

Enter Pakistan’s ambassador to the U.S., Husain Haqqani, who got on the phone with The Atlantic‘s Jeffrey Goldberg to say: “If Whitey Bulger can live undetected by American police for so long, why can’t Osama Bin Laden live undetected by Pakistani authorities?”

If the Pakistani ambassador was saying this to the press, one can only imagine what he was telling U.S. government officials behind closed doors. Haqqani may have said more than he intended, for it is as hard to believe that his country’s intelligence agency knew nothing of Bin Laden’s whereabouts as it is to believe that the FBI knew nothing of Bulger’s. But in all events Haqqani had picked a scab.

That conversation was reported on May 2. Ten days later, Mueller had a sit-down with President Obama, who afterward proclaimed the director had “set the gold standard” and deserved another two years of public service. The extension had no precedent since Congress established a 10-year term limit for the FBI director in 1972, a reaction to the long, vicious reign of J. Edgar Hoover.

Still, if Mueller was smart, he might have felt some pressure. Congress would have to vote to reconfirm him. It did so almost exactly a month after the FBI stunningly captured Whitey Bulger, on June 22, 2011.

[End, Part 1]