Flanagan was born on October 20, 1946, and raised in Manhattan, New York. Both his parents were Irish. His father was an advertising executive and his mother a teacher, stockbroker, and antique dealer. Flanagan was introduced to politics by his parents who supported Illinois Democratic governor Adlai E. Stevenson, an unsuccessful presidential candidate in 1952 and 1956. From early on Flanagan felt the pull of militancy. He recalls, "I know that from a fairly early age, 11 or 12, I had really come to admire Fidel Castro. When he stood up to the United States, I thought that was a great thing." Flanagan grew up in a house of privilege with a summer residence in tiny Southampton Long Island. During those years from high school to college, he spent his days as a caddy at the National Golf Links of America.
During the 1960s, Flanagan attended Columbia University in New York, where he was a member of Students for a Democratic Society. Flanagan studied philosophy and economics at Columbia where he was a C student. Whatever passions academics failed to arouse, however, the rising opposition to the Vietnam War supplied. "That was the turning point for me," he says. "Being in New York, being at Columbia during the Vietnam War, you could not be oblivious to what was going on. People were lining up on one side or the other. And so I took my stand." Flanagan was one of the members that helped seize the mathematics building on the Columbia University campus. The 1968 Columbia Student Revolt involved students shutting down the campus by seizing buildings to attract attention for their cause. SDS confronted the university's involvement with the Institute for Defense Analysis, who provided research on the military used in Vietnam, and the university gym located in Harlem, which would not benefit the African-American neighborhood population. In 1969, Flanagan joined Weatherman, a radical splinter group of the SDS, later known as the Weather Underground Organization.
On October 8, 1969, Weatherman staged its first act of public aggression, at a rally in Chicago called the Days of Rage. The rally was staged in opposition to the Vietnam War, and its slogan was "Bring the War Home". Members gathered at Grant Park to listen to speeches by SDS leaders about Che Guevara and the world revolution. The rally turned to the streets of Chicago, where participants vandalized businesses, smashed car windows and blew up a statue of a policeman known as the Haymarket statue. During the rally, Flanagan had a physical encounter with then 35-year-old lawyer Richard Elrod that left Elrod with a broken neck and partially paralyzed from the neck down. Both men report different testimonials of what transpired that day. Flanagan stood trial for "attempted murder, aggravated battery, felonious mob action, and resisting arrest" and was acquitted on all charges. Michael Rollins, a reporter for WCFL who was interviewing Elrod just before Elrod broke away to chase Flanagan, supported Flanagan's description of what happened. Although he told his story to the police and the state's attorney's office, he was never called before the grand jury. Richard Hinchion, 43, an insulating contractor from Munster, Indiana was another eyewitness supporting that version.
Weather Underground Organization
On March 6, 1970, Diana Oughton, Terry Robbins, and Ted Gold, members of Weatherman died in a Greenwich Village townhouse explosion when a nail bomb detonated after members purchased two 50-pound cases of dynamite. It was explained later that the bombs were to be detonated at a non-commissioned officers' dance at Fort Dix. In an interview, Flanagan suggested that he helped one Weatherman member, Kathy Boudin, who later served 22 years in prison for felony murder and robbery, flee New York City after police investigations placed her in the townhouse during the time of the explosion. Following the townhouse deaths, many members of Weatherman went into hiding, forming Weather Underground Organization, said to be responsible for a series of bombings of US state and federal buildings between 1970 and 1975. In the documentary filmThe Weather Underground, Flanagan admits to participating in Weather's bombings during the 1970s. During a memorable moment in the film, Flanagan states, "When you feel you have right on your side, you can do some horrific things". After resurfacing from the underground, Flanagan joined the Prairie Fire Organizing Committee, the above-ground wing of Weather Underground Organization. Like many members of the Weather Underground Organization, Flanagan was never jailed for his involvement 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 as a contestant on the television game show Jeopardy!. Flanagan continued his interest in trivia, hosting a weekly trivia contest at his bar, the Night Café in Manhattan, which he ran for fifteen years. Forced out of the space due to increased rent, the Night Cafe closed in September 2007.