On October 8, 1969, the Weathermen staged their first act of public aggression, a rally in Chicago called the “Days of Rage.” The rally was staged in protest of the Vietnam War, and its slogan was “Bring the War Home”. The rally turned to the streets of Chicago where participants vandalized businesses and car windows and blew up a statue of a policeman. During the rally Flanagan had a physical encounter with 35-year-old lawyer Richard Elrod that left Elrod with a broken neck and partially paralyzed from the neck down. Flanagan stood trial for "attempted murder, aggravated battery, felonious mob action, and resisting arrest". When eyewitnesses offered conflicting testimony of the event, Flanagan was acquitted.
In 1970, three members of the Weathermen died in a Greenwich Village townhouse when a bomb accidentally exploded. Flanagan has suggested in one interview that he helped one Weatherman, Kathy Boudin, who later served 22 years in prison for felony murder and robbery, flee New York City after police placed her in the townhouse during the time of the explosion. Following the townhouse deaths, many members of the Weathermen went into hiding, forming the Weather Underground, which carried out a series of bombings of US state and federal buildings between 1970 and 1975.
In the documentary film The Weather Underground, Flanagan admits to participating in the Weathermen’s bombing campaign in the 1970s, though in the most memorable moment of the film Flanagan laments, “When you feel you have right on your side, you can do some horrific things.” After surfacing from the underground, Flanagan joined Prairie Fire, the above-ground wing of the Weathermen. Like many members of the Weather Underground, Flanagan was never jailed for his involvement in the Weather Underground due to the illegal evidence-gathering tactics of the FBI’s COINTELPRO program.
In the 1990s, Flanagan played pool on a professional billiards circuit and worked as a carpenter and bartender. In 1996 he won $23,000 on the game show Jeopardy! Flanagan continued his interest in trivia, hosting a trivia contest at his bar the Night Café in Manhattan, which closed in September 2007.