On 30 November 1984, Patrick Nee picked up 32-year-old John McIntyre from a bar and lured him to Nee's house with a case of beer and a promise of a party. At this time, Nee knew that McIntyre was cooperating with federal law enforcement against Nee for the smuggling of 7.5 tons of automatic weaspons, machine guns, rocket launchers, plastic explosives, bullet proof vests, and ammunition aboard the Valhalla. Nee also knew that just 17 months prior, Arthur Barrett had been lured to Nee's house and murdered. Barrett's body remained where Nee had buried it in the cellar of Nee's house into which he was now luring McIntyre. Nee knew that his associates sat in his house armed with machine guns waiting for Nee to return with McIntyre. Like Barrett, McIntyre was murdered in Nee's house and buried in Nee's cellar beside the corpse of Barrett. Nee remains a classic suspect in the murder of McIntyre. He was the last person seen in public with McIntyre. He had the motive, opportunity and means to murder McIntyre. His intent to murder McIntyre is evident in the method he employed that copied his murder of Barrett the year before.

Between 1999 and 2003, US Attorneys in Boston immunized two of Nee's associates who were present with him at his house that day and thus had proof of McIntyre's murder. Despite relying on these witnesses to indict other associates who were present, the US Attorneys decided not to indict Nee. The US Attorneys' willingness to ignore Nee's involvement in McIntyre's murder has fueled speculation that Nee is a protected federal infomant.

Nee fled Boston after being informed by Bulger that Federal agents were looking for him. After several years in hiding, he was arrested in 1987 and served an 18-month sentence in Federal prison. Although Nee claims Bulger told him to flee, it is suspected that his federal law enforcement handlers in the US DOJ advised him to flee.[citation needed] The statutory sentence Nee faced for possessing and smuggling 7.5 tons of automatic weaspons, machine guns, rocket launchers, plastic explosives, bullet proof vests, and ammunition was a life sentence. Bulger was convicted in 2013 of possessing one of the same guns that Nee had aboard the Valhalla and he received a life sentence. The fact that Nee received only an 18-month sentence at a soft federal facility instead of the mandatory life sentence has fueled speculation that Nee was a federal informant.

After his release in 1989, Nee was disgusted by McIntyre's murder and, motivated increasingly by Irish nationalism, he decided to cut his links to Bulger. He put together a crew of his own and began planning Armored car robberies to raise money for the IRA. He was arrested by the FBI during an armored car robbery in Abington, Massachusetts on January 13, 1990. He was sentenced to 37 years in Federal prison[citation needed], but was released after April 2000.[9]

When Nee was arrested in Abington, Massachusetts on January 13, 1990, Nee was masked and in possession of another machine gun which again carried a mandatory life sentence. Instead of being sentenced to the minimum mandatory life sentence, Nee was given a sentence of 37 years. Federal Sentencing Guidelines at that time prohibited early release or credit for "good behavior" in a federal prison. Despite being convicted for a second time of charges that mandated a life sentence, Nee only served about 8 years at "soft" federal facilities and was released 29 years earlier than his parole date. The US Attorney's Office in Boston has refused to explain Nee's early release and why they failed to oppose it. Nee's release after eight years of what was a mandatory minimum life sentence fueled speculation that he is a protected federal informant