This 2002 post discusses Joseph Salvati, who spent 30 years in prison for a crime he didn't commit. Agents in the FBI's Boston office knew he was innocent but wanted to protect the informants who actually committed the crime.

This 2004 post reported the details of a lawsuit accusing Connolly of telling Bulger that John McIntyre was ratting him out to federal authorities. McIntyre disappeared in 1984, soon after Bulger obtained that information. His body wasn't found until 2000.

Connolly was convicted in 2002 of racketeering, a conviction based in part on a tip he gave to Bulger that enabled him to avoid a 1995 arrest. Bulger remains a fugitive to this day. Connolly was sentenced to ten years.

The Hartford Courrant has this to say about the lessons we must learn from Connolly's actions:

It is deeply unsettling to think that a major office of the nation's most important law enforcement agency had been pervasively compromised and corrupted. That it could happen should give serious pause. It is a particular challenge of criminal investigation to lie with dogs and not get fleas, to run informants and pursue wrongdoers without succumbing to their lures. The FBI has revised its informant guidelines in light of the Boston cases but must still push for checks that will dissuade the next John Connolly from crossing the street.

Informants should never be given a pass to commit crimes. Apart from the slippery slope (how many smaller crimes should the FBI overlook in its effort to capture a bigger criminal?), the FBI is in the business of law enforcement, not crime assistance. It really isn't possible to lie down with dogs and not share their fleas.