Jeje Odongo was captured soon after the first NRA operation and was imprisoned in Luzira Maximum Security Prison.
In 1996, he was selected to replace Colonel Sserwanga Lwanga as the Political Commissar in the Uganda People's Defense Force (UPDF).
In 1998, he resigned his parliamentary seat and his cabinet position and was appointed Commander of the Army, taking over from Major General Mugisha Muntu.
[7] In May 2008, Jeje Odongo graduated with the degree of Master of Arts in International Relations and Diplomacy from Nkumba University.
A controversy arose when he greeted President of the European Commission, Ursula von der Leyen, only after an intervention by Emmanuel Macron, which was considered a misogynistic attitude.