The Martyrdom of John Connolly

Corrupt FBI agent John Connolly earned infamy—and a 10-year jail sentence—for aiding über-gangster Whitey Bulger. But in his upcoming murder trial, the real bad guys will be the ones given sweetheart deals to present their shaky testimony against him. (The prosecutors are no angels, either.) The case against the case against a man the Justice Department seems set on punishing for others' sins.

john connolly

Illustration by Sean McCabe

In a Miami maximum-security prison, John Connolly spends 23 hours a day alone in a 10-by-11-foot cell. The former FBI agent writes endlessly on yellow legal pads, the penmanship shaky because guards, viewing pen shafts as potential weapons, allow inmates only thin, flexible ink cartridges. His letters run to 30 pages and are fairly damp from the bile. When letters aren’t enough, he calls collect, his voice rising at the mention of his enemies: federal prosecutors, the cops who investigated him, and the mobsters who took deals to testify against him. Connolly calls them all “liars” and “bastards.”

“I am a prisoner of war,” he writes.

He entered that war enthusiastically, when breaking up the Mafia was a national priority. A product of South Boston’s projects, with contacts in the Irish underworld, Connolly was the greatest of G-men, bringing down Boston’s Italian mob in the 1980s nearly by himself, or so it would seem from the acclaim Connolly received from the media—appearing always with coiffed black hair, stylish suits, and French-cuff shirts—and from FBI headquarters in DC.

But a decade after it was won, that war, or at least Connolly’s starring role in it, turned out to have been dirty. He developed and handled two secret informants: Irish mobster James “Whitey” Bulger and Bulger’s partner, Stephen “the Rifleman” Flemmi. In May 2002, a federal jury convicted Connolly of racketeering and obstruction of justice—of being part of Bulger’s mob—and of tipping Bulger and Flemmi to their secret indictment in 1994. (Flemmi claims he and Bulger gave Connolly $235,000 for his services, all told.)

Bulger fled Boston before the cops came with arrest warrants. Flemmi didn’t get out in time. When it became clear that no one in the FBI or Justice Department could protect him, Flemmi finally agreed to talk in 2003. But Connolly never has. And because he didn’t cut a deal—like so many mobsters who testified against him in exchange for lighter sentences—because he “refused to lie,” he says, as the Justice Department wanted him to, Connolly is serving a maximum sentence of 10 years.

“The Department of Justice threw him under the bus,” says Bob Fitzpatrick, the commander of the FBI’s organized-crime squad and Connolly’s former boss.

The charges he was convicted of, however, pale in comparison with those he faces today. This month Connolly is scheduled for trial on a claim that in 1982 he plotted and committed murder in the first degree, by telling the Bulger mob that if a potential witness sang they were all going to prison.

At Connolly’s last pretrial hearing in July, the black hair had gone gray, the face was puffy, and the once-flashy wardrobe was reduced to a rumpled red jumpsuit. Under the judge’s questions, he showed none of his trademark arrogance or the anger he lets slip during collect calls. Connolly instead nearly entreated the judge to see things his way. “I’m innocent. I’m pleading not guilty.”

Connolly says he’s being framed by the same justice system that once commended his work, which is also the same justice system that failed to prosecute the misdeeds of his fellow agents. This trial, like the last, will hinge upon one corrupt supervisor, but also career criminals who have dealt themselves out of the death penalty or long prison sentences by agreeing to testify. If convicted, Connolly is likely to spend the rest of his life in prison. And yet the mobsters who’ve become partners in his prosecution collectively account for about five dozen murders and are, with one exception, out on the street or headed there soon. It appears John Connolly must atone for the sins of everyone: the mobsters, the Justice Department, and the FBI.


I picked up the Whitey Bulger beat as a television reporter at WGBH in 1988.

At the time, I was reporting the case of 75 State Street, in which real estate emperor Harold Brown alleged in court papers that Thomas Finnerty, a lawyer, had used his relationship with his law partner, former state Senate President William Bulger, to extort money. Brown later dropped his accusation; rumors attributed the decision to fear of violent retaliation by William’s brother, Whitey. Even if the rumors were groundless, they spoke to the terror Whitey could inflict.

Covering organized crime and corruption in the FBI had the feel of theater; our motto at WGBH was “We don’t cover murders. We cover assassinations.” I claimed the same beat after I moved to Channel 5 in 1991, in part because none of the other reporters had assembled (or cared to assemble) the stash of wiseguy files needed to tell the difference, say, between “Jimmy the Weasel” and “Jimmy Blue Eyes.” Ask me about the murder of Teddy Deegan in 1965 and I could tell you about the whole menagerie: Joe the Seagull, Ronnie the Pig, Jimmy the Bear, Romeo the Goat, Joe the Horse.

Along the way, I spent so much time with cops that I started acting like one. I did surveillance, tracked Bulger associate Pat Nee after he got out of prison, figured out his daily schedule, and ambushed him outside his house with my cameraman early one morning in April 2000. I asked him about the recently discovered remains of Bulger victims. I said, “John McIntyre’s brother wants to know what you did with his fingers and toes.” Nee never answered my question.

But Frank Salemme did. The former head of the New England Mafia was thought to be in the witness protection program; I found him at the Busy Bee diner in Brookline in 2004. I followed him for a week, learned his comings and goings, and then introduced myself on-camera one day as he left the Bee. Over several days and many meals, he talked to me about his “clips,” as if we were two gardeners pruning roses. Salemme touted his public service of testifying in late 1999 against Connolly, a move that, ultimately, lessened his own prison time.

Breaking stories and sitting with Mafia dons had an electric thrill, but the deeper I got into the landscape, the more squalid it became. Over the years I’ve seen the broken bones of young men and women unearthed at once-secret burial grounds, spoken with the families who buried what was left, and talked to old gangsters and government witnesses who did the killing. The value in reporting all this, I told myself, was how much of it traced back to dirty deals, dirty prosecutors, and dirty cops. I kept waiting for the full acknowledgment of what went wrong in Boston. I am still waiting.


This was the deal the FBI struck in 1975: To rid Boston of the Italian mob, John Connolly would act as a liaison for Whitey Bulger and Stephen Flemmi, who would in turn rat out the Mafia, for whom the pair sometimes worked. It was a great deal for Bulger and Flemmi; for their cooperation, the evidence suggests, the Justice Department looked the other way. Connolly says Bulger and his crew had authorization from the Justice Department to continue their crimes: loansharking, gambling, and extorting bookies. As long as they committed no violence, they wouldn’t be prosecuted. The deal worked for the government, too. The 1980s saw a parade of handcuffed Mafia foot soldiers, capos, and dons escorted into custody, with Connolly invariably front and center before the waiting TV cameras.

If you were around then, you probably know all this. You probably know how Connolly and his supervisor became too close to Bulger and Flemmi, were corrupted by them, that even as the FBI brought to its knees the Italian Mafia, it allowed the far more sinister force of Whitey Bulger to metastasize. You probably know from 10 years of newspaper stories, TV news spots, magazine pieces, and a shelf of Bulger books (not to mention The Departed, the Oscar winner loosely based on the Bulger-Connolly story) that Connolly was the law on Bulger’s side.

Few public characters have faced such an overwhelming presumption of guilt as John Connolly. But he didn’t act alone. In fact, if Connolly belongs in prison, so, too, do a number of other former FBI agents.

Start with John Morris. He was Connolly’s supervisor on the organized-crime squad. Thin, dour, formal, and cagey, Morris drank too much and talked too much over dinner with the mobsters. He admitted to taking $7,000 in bribes from Bulger and Flemmi, tipping them off to wiretaps, and warning them about an informant named Brian Halloran who detailed one of Bulger and Flemmi’s murders for the FBI. (Bulger subsequently killed Halloran.) After Bulger fled in 1995, and the investigation into FBI wrong-doing began in earnest, Morris received immunity from the Justice Department. Bob Fitzpatrick, a high-energy product of the tougher streets of New York, came to the Boston bureau as Connolly and Morris’s boss in the early ’80s. He says Morris got immunity because he had better connections than Connolly to high-ranking Justice Department and FBI officials. If need be, Morris could give up his own superiors, because they weren’t clean, either.

One of them was Jeremiah T. O’Sullivan, the lead federal prosecutor for the organized-crime strike force in Boston. In 1978, Bulger and Flemmi were about to be indicted with numerous associates in a horserace-fixing case. O’Sullivan took their names out because he and headquarters wanted to keep Bulger and Flemmi working as informants. In effect, O’Sullivan gave them a pass for their crimes and more reason to believe they had immunity from future prosecution, as Connolly has insisted. “Is that obstruction of justice? You better believe it,” Bob Fitzpatrick concludes.

Fitzpatrick himself has long fought to clear his name after, he says, he was forced out of the FBI for attempting to root out corruption. He opposed the use of Bulger as an informant. In court cases and depositions, he has testified that agents in the organized-crime squad stole files from another team investigating Bulger and the people who might be tipping him off. Fitzpatrick testified that the special agent in charge of the Boston office, James Greenleaf, had leaked the identities of two men who were telling the FBI about Bulger’s crimes. One of them, John McIntyre, was subsequently tied up, strangled, and shot in the back of the head by Bulger in 1984. Greenleaf would not comment for this story.

Fitzpatrick can name at least 10 agents in Boston in the ’70s and ’80s he believes were corrupt. Kevin Weeks, who’s been called Bulger’s surrogate son, recalls Bulger bragging that he could call on six FBI agents any time who “would willingly hop in the car with a machine gun.” Not for nothing did Bulger wake up every morning, look out his window, and say, “‘I own this town,'” Weeks told me. The FBI and Justice Department were so entangled with Bulger and Flemmi that the two organizations fought the state police and Drug Enforcement Administration’s investigation of Bulger and Flemmi, and resisted the efforts of federal prosecutor Fred Wyshak to indict the pair. Only when the state police and DEA threatened to go public with this did the FBI and Justice Department join the case.

After Bulger and Flemmi were outed as FBI informants in 1997, Flemmi claimed he couldn’t be prosecuted: By virtue of his status as a top-echelon informant, he had immunity. Federal Judge Mark Wolf conducted months of hearings in his Boston courtroom. Wolf would later describe an extraordinary effort by the FBI to cover up “serious impropriety if not illegality”: Agents received gifts and money from mobsters, and warned them about the cops who were on their trail. In response, U.S. Attorney General Janet Reno appointed a special outside prosecutor, John Durham, to investigate the mess. But Durham wasn’t exactly the cavalry coming to the rescue.


At the time he was assigned the case, Durham, a slightly built career prosecutor, looked like the late comedian Wally Cox with a comb-over. At a press conference in October 2000, I asked Durham if he would pursue other compromised FBI agents. Durham said he would, but cautioned that the statute of limitations for some crimes might prevent him from bringing charges.

Whatever he found, though, he would account for in an official report. Another journalist asked when this report would be turned in. Durham said three to four months. In the spring of 2001, I asked Durham where the report was. He just smiled in response. In May 2002, after Connolly’s conviction, Durham held another press conference. “Nobody in this country is above the law, an FBI agent or otherwise,” he said. I asked what happened to his report, his promised full accounting. No answer.

Eight years later, Durham has yet to make good on his vow. From 2000 onward I have tried to secure an answer from Durham by phone or letter. He has never responded. (And efforts to reach him for this piece were unsuccessful.)

Four state and local cops, and ex-agent Bob Fitzpatrick, have told me they were each interviewed by Durham’s team. Each laid out evidence of wrongdoing by FBI agents in the Boston office, along with names of those who could corroborate their statements. But in every case, the cops say, the account of the interview submitted to Durham’s office (which the cops got to see) routinely failed to note their most serious allegations.

After Connolly, Durham never prosecuted another FBI agent. The state police–DEA team had developed all but one of the major witnesses Durham used to convict Connolly; its members were convinced they had enough evidence to nail other wayward agents. They expected Durham to push forward. “Don’t tell me some other FBI supervisors couldn’t be held accountable,” says retired state police Colonel Tom Foley, who led the team. “There were a number of areas where [Durham and his investigators] could have gone farther than they did.” Foley’s team and the prosecutors they worked with say Durham is a company man who knew his assignment: Convict Connolly and contain the damage.

During Connolly’s 2002 trial, Durham relied heavily on a witness the state police and DEA had warned him against: Frank Salemme, the don of the New England Mafia. Durham had first turned to Salemme in late 1999, as the statute of limitations for Connolly’s alleged crimes was running out. Salemme, who’d been arrested in 1995 in the same racketeering case targeting Flemmi and Bulger, agreed to testify that Connolly tipped off the three of them about their impending indictments, so they could skip town.

But the state police–DEA team believed Salemme had lied about murders he’d committed, and therefore shouldn’t be trusted as any sort of witness. Tom Foley says he and federal prosecutor Fred Wyshak told Durham of Salemme’s falsehoods and strongly advised him against using Salemme at Connolly’s trial.

Durham went ahead anyway. During courtroom testimony, Salemme denied his role in several murders. After Connolly’s conviction, during Salemme’s request for an early prison release, Durham praised Salemme, saying he had been as good as his word. Just under two years later, with Wyshak serving as prosecutor, Salemme was indicted for perjury. He later pleaded guilty to making a false statement.

Durham’s career has only climbed since he secured Connolly’s conviction. Earlier this year, U.S. Attorney General Michael Mukasey tapped him to lead a criminal investigation into the destruction of CIA interrogation videotapes involving Al Qaeda suspects. Newspapers across the country cited Durham’s tenacious efforts in the Connolly case as proof of his moral compass.


To understand the current murder charge against Connolly, it’s best to reexamine the murders that preceded it, and the men who carried them out. John Martorano, a.k.a. “the Basin Street Butcher,” killed 20 people in his career, the last few for Bulger and Flemmi. His 19th victim, an Oklahoma man named Roger Wheeler, was the legitimate owner of a pari-mutuel betting franchise in Miami called World Jai Alai that Martorano and the Bulger mob wanted to subvert. One afternoon in May 1981, Wheeler left his country club in Tulsa. Martorano followed him on foot. He wore a fake beard and held a paper bag and a white towel over a revolver. As Wheeler got in his car, Martorano shot him from 3 inches away.

If Martorano ever got queasy about killing someone, though, it was victim number 20. Number 20 was a good friend, John Callahan, a Boston accountant who lived a dichotomous life: working in the Financial District by day, hanging out with gangsters by night. Callahan was the one who had wanted Roger Wheeler out so he could run World Jai Alai himself. Callahan first tried to enlist his friend Brian Halloran, a Boston gangster, as the killer, but Halloran refused. So Callahan approached Martorano and offered him, Flemmi, and Bulger part of the business after he took over.

Some months after Wheeler’s murder, the gangster Halloran, trying to escape his own jam with the law in Boston, began dishing details of the World Jai Alai killing to the feds. FBI boss Bob Fitzpatrick wanted Halloran in the witness protection program. But John Connolly entered the picture, attacking Halloran’s credibility, saying Bulger and Flemmi called Halloran a drugged-out liar. The decision was left to Jeremiah O’Sullivan, the same federal prosecutor who, in 1978, protected Bulger and Flemmi from the race-fixing indictment. Halloran was dumped back onto the streets in May 1982. That same month Bulger and a second gunman ambushed him on Northern Avenue and killed him.

By July 1982, more than a year after Wheeler’s murder, and two months after Halloran’s, detectives from Florida and Oklahoma suspected Callahan was linked to both cases and raced to find him, fearing he could be the next victim. Back in Boston, Bob Fitzpatrick now thought he had a major leak within his FBI ranks and quickly set up an interview with Callahan for the first week of August. But Bulger, Flemmi, and Martorano got to him first.

Martorano says he received the order to kill Callahan because Connolly allegedly told Bulger, “We’re all going to jail for the rest of our lives if they catch up with Callahan [and he sings].” And so when Callahan flew down to the Fort Lauderdale Airport on July 30, Martorano was waiting for him curbside. Martorano got out of the van he was driving, greeted Callahan, and put his luggage in the back. As Callahan sat down in the passenger seat, Martorano reached around and shot him in the back of the head. He probably died before he noticed that the car floor was covered in plastic to catch the blood. Afterward, John Connolly filed a report attributing Callahan’s murder to Cuban or Libyan drug dealers.


John Martorano lived in Florida for the next 13 years. He’d been a fugitive since fleeing impending federal charges in 1978. In January 1995, after Bulger and Flemmi’s indictment, the state police–DEA team went to Boca Raton and found Martorano living with a cleaning lady whom he’d brought from Boston, and the couple’s son.

Years later, sitting in a federal courtroom in Post Office Square beside Stephen Flemmi, Martorano learned that both Flemmi and Bulger had been government rats. Martorano had murdered rats. Upset, he flipped on his partners, cut a deal with the government, and described the World Jai Alai murders in Oklahoma and Fort Lauderdale and a long history of other killings in Boston. He testified that the warning about Callahan had come from Connolly.

In 2003, Flemmi agreed to cooperate with the government and laid out the details of the Wheeler, Halloran, and Callahan murders. By implicating Connolly, Flemmi enabled the state of Florida to charge Connolly with murder in the first degree and conspiracy to murder in Callahan’s death. The oft-delayed trial will finally get under way September 8. Judging by testimony from Connolly’s 2002 trial, civil depositions, pretrial hearings for this month’s affair, and interviews with cops and lawyers, the outline for the prosecution seems clear. Flemmi will testify Bulger told him of Connolly’s warning: namely, if Callahan talked to detectives, Callahan would give everyone up. Flemmi will also testify that he then checked with Connolly and heard the same thing. Martorano will testify that, after they told him what Connolly had said, Bulger and Flemmi convinced Martorano that Callahan had to be killed.

It’s not a strong case for the prosecution: There’s no explicit message from Connolly to kill Callahan. Furthermore, consider the government’s witnesses. Flemmi has pleaded guilty to 10 murders, including those of a girlfriend and a stepdaughter. For testifying this month, he’s been spared the death penalty in Florida and Oklahoma. Martorano also avoided the death penalty for his testimony, but in addition got his sentence reduced to 12 years, which comes to seven months for each of his 20 murders. The federal judge presiding at Martorano’s sentencing told him he was “a calculating opportunist.” When Martorano got out of prison in 2007, the feds gave him $20,000 to start a new life. (Martorano is currently working with a Hollywood screenwriter to tell his life story.)

Still, Assistant U.S. Attorney Fred Wyshak says the deals with Flemmi and Martorano were the lesser of two evils. The government couldn’t have charged Connolly with Callahan’s murders without their cooperation. To bolster the case, the prosecution will try to convince jurors of Connolly’s guilt by showing the murder in Miami as part of a pattern. Connolly warned Bulger about rats; Bulger and company murdered rats; Connolly filed false FBI informant reports to draw attention away from the real killers. Connolly therefore had to have known that by talking to Bulger he was getting Callahan killed.

But strangely enough, Martorano never mentioned Connolly when he first began cooperating with the government. According to Miami-Dade detective Ram Nyberg’s report in December 1999, “Martorano had no idea of anyone else besides [himself and] Bulger and Flemmi who were involved in the conspiracy to kill Callahan.” At a deposition in March 2006, the detective reaffirmed his earlier report: “Neither of Mr. Martorano’s proffers included any information on John Connolly.”

This is why the defense, too, hopes to use Martorano and Flemmi to its advantage. Flemmi has an established record of lying. During court hearings in Boston in the late ’90s, he testified that the tip to escape arrest in 1995 had come not from Connolly, but from FBI supervisor John Morris. (It was Connolly who told Flemmi to tell that lie, a federal jury concluded.) Many times, Flemmi was accused of perjury by the same prosecutor, Fred Wyshak, who will help the state of Florida present Flemmi as a witness this month. But Flemmi has been consistent on one point: He’s never said Connolly told him, or Bulger, to murder anyone. During a deposition in New York in April 2005, an attorney asked Flemmi, “Did [Agent Connolly] ever suggest to you directly or indirectly that certain people should be killed?”

“No,” Flemmi said. “He gave information for Bulger. Bulger interpreted it the way he wanted to interpret it.”

This may not be enough to convict him. But that doesn’t mean jurors won’t wonder how much John Connolly is keeping to himself. He is the only one, after all, who could give a nearly full accounting of the Bulger case. But he has refused to disclose anything. At the pretrial hearing in July, he testified that the government offered him a plea deal three years ago. He would have served only fiv
e years for murder. All he had to do was talk. Because he won’t, the irony is that John Connolly, an ex–FBI agent, is the only person in this sordid saga to honor the mobster’s code of silence.