In 1989, Charles Taylor's
National Patriotic Front of Liberia (NPFL) invaded Liberia from Côte d'Ivoire, where Bockarie was living at the time. However, Bockarie did not join until later that year, when he met recruits who were talking about taking action in Sierra Leone. He went with the group to join guerrilla training exercises held along the border of Sierra Leone and Liberia. He was officially a part of the newly formed RUF in 1990, and was a part of the initial incursion into Sierra Leone in 1991. In 1992, Bockarie made the move into the upper leadership of the RUF, becoming Battle Group Commander, answerable only to the Battle Field Commander and Foday Sankoh, the leader of the RUF. In March 1997, Sankoh fled to
Nigeria, where he was put under house arrest, and then imprisoned. From this time until Sankoh's release in 1999, Bockarie performed the task of director of military operations of the RUF, with alleged advice from Charles Taylor. During this time, Sankoh worked with the
Armed Forces Revolutionary Council (AFRC), the group of
Sierra Leone Army (SLA) officers which had overthrown President
Ahmed Tejan Kabbah on 25 May 1997, and held the presidency until February 1998. Bockarie held the position of Chief of Defence Staff in the RUF/AFRC led junta government. In January 1999, Bockarie along with AFRC commander
Johnny Paul Koroma planned and made a devastating attack on
Freetown, the capital of Sierra Leone. On 7 July 1999, the
Lomé Peace Accord was signed by president Kabbah and RUF/AFRC leader Sankoh, after Sankoh had gotten the consent of his field commanders, including Bockarie. However, tension continued in Sierra Leone, especially due to a new rebel faction called the
West Side Boys, leading to more attacks in and around Freetown in May 2000. Bockarie was reluctant to ask his forces to disarm amidst the new tension, and he and Sankoh had a falling out in the early spring of 2000. By the time Freetown was again embroiled in violence, Bockarie had fled to Liberia's capital,
Monrovia. Rebel forces did not begin to disarm until 2001. ==Indictment for crimes against humanity==