The answer the FBI came up with was to have a fall guy. It put it out and the media went along with it that Connolly was a rogue agent. Somehow he was not supposed to be involved with those two individuals even though it was his job at the FBI. it wasn’t that he was doing it in secret; to be a Top Level Informant a person had to be approved at the highest levels of the FBI down through the agent in charge, his deputy and the agent’s supervisor. In other words what Connolly was doing, namely: protecting his informants was known and approved by the FBI command structure. They wanted him to do it.
This was all obfuscated by the time John Connolly was brought to trial thanks to the media’s connection with the US Attorney’s office in Boston. One person who knew about the Top Echelon Program was was Ralph Ranalli who in 2001 wrote the book Deadly Alliance with the sub-title “The FBI’s Secret Partnership With The Mob.” Ranalli was a staff writer for the Boston Globe and Boston Herald. His acknowledgements showed he wrote the book with the help of many who were involved in the prosecution, writing about, or demonizing Connolly. As such, he too missed the “rogue agent” plan.
Among those Ranalli relied on for information was FBI assistant agent in charge Robert Fitzpatrick who pleaded guilty to 12 counts of an indictment charging him with
perjury and obstruction of justice in connection with his testimony at the 2013 trial of James “Whitey” Bulger. Fitzpatrick wrote a book which he claimed things he would later say were not true and contained other things that I found ridiculous and wrote about.
On one occasion Fitzpatrick suggest to me that I had taken the title of my book from something he wrote. I laughed. I explained how I arrived at the title. I also learned later doing some research on the FBI that embarrassing the FBI was the thing J. Edgar Hoover would not abide. I found a book written in 1972 by an agent that had the title “Don’t Embarrass the Bureau.” That was the first commandment. The first thing taught to all agents that they can do whatever they want as long as they don’t embarrass the job. During the days when the agents did black bag jobs to plant bugs they were told it was fine to do them but if they got caught (and couldn’t fix it quietly) the FBI would call them rogue agents.
Why did Connolly limit his defense and not disclose what his job on the FBI was supposed to be? That has always been a mystery to me. I sometimes speculate that Connolly never understood the FBI was betraying him even though it was assisting the prosecutor. He often attacked the Department of Justice as the culprit. That being the case he did not want to embarrass the job by saying “yes, I did what I did because I was supposed to do it.”
I’m also convinced he believed he would be acquitted. He told me during the trial something to the effect, “I did nothing wrong and I know of no one in the FBI who did anything wrong.” Unaware the first commandment of the FBI I did not have the knowledge to tell him that whether he did something wrong or not did not matter. The FBI was embarrassed the public knew he was the handler of Flemmi and Bulger. It needed to wash its hands to suggest it was blameless in his actions. It made Connolly into a rogue agent with the help of his supervisor who was John Morris who would testify against Connolly.