Indjai emerged from within the ruling junta during the destructive civil war which lasted from June 1998 to May 1999. In 1999, Indjai was named deputy commander of the northern military zone led by Tagme Na Waie. In 2004, Tagme was promoted to the top army post after the death of army chief General Verissimo Correia Seabra, and Indjai became leader of the northern military zone. In 2006, Indjai was promoted to Colonel as a result of his leadership in the war against a Senegalese separatist group from the Casamance who had set up camp in Guinea-Bissau. In November 2008, Indjai was promoted to brigadier general and deputy army chief.