In 1965, Sekou joined the Organization of Afro-American Unity (OAAU), founded by Malcolm X. After Malcolm's death the OAAU was not going in the direction he wanted and in 1967 he was looking at the Black Panther Party. In early 1968 he helped build the Bronx Black Panther Party. On January 17, 1969 two Panthers, Bunchy Carter and John Huggins, were killed by members of US Organization on the UCLA campus, and a fellow New York Panther who was in police custody was brutally beaten. Sekou was informed that police were searching for him in connection with a police shooting. The confluence of these events convinced Sekou to disappear from public-facing organizing and join the black underground with the Black Liberation Army.

Sekou Odinga remained underground, partaking in revolutionary clandestine activity for twelve years until his capture. Upon being captured in 1981 he was charged with six counts of attempted murder, nine predicate acts of Racketeering Influenced Corrupt Organization (RICO), stemming from his involvement in the escape of Assata Shakur from prison and the Brink's armored car robbery. He was convicted in 1984 and sentenced to a consecutive twenty-five years to life state sentence and a forty-year federal sentence. Burns' convictions were affirmed by the United States Court of Appeals for the Second Circuit in March 1985. Odinga was released from prison on November 25, 2014