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.