[6] In the Battle of Kampala of 17–26 January 1986, Mugisha initially led the frontline NRA troops after his superior Pecos Kutesa allegedly fell ill.[7] As the rebels advanced deeper into the city, he continued to fight alongside his troops, reportedly displaying considerable bravery under fire.

In 2000, he attended the Platoon Commander Course at the Sierra Vista Military Academy in Arizona, United States of America.

From March 2001 to December 2001, he was Deputy Chief of Military Intelligence and Security at the rank of lieutenant colonel.

The next year, in 2006, he attended the Senior Command and Staff Course at the Army War College at Mhow, Madhya Pradesh, India, in 2006.

[3] From May 2013, he was replaced as Joint Chief of Staff by Major General Wilson Mbadi and assigned to the position of commandant of the newly established "National Counter Terrorism Center".