In addition to this, Tumukunde was promoted to the rank of lieutenant colonel and appointed Chief of Personnel and Administration. He is credited with having introduced the promotional exams system (PROMEX) for officers in the army which remains in use to date. In 1998, Tumukunde was again promoted to the rank of colonel and appointed chief of military intelligence and security. His tenure was arguably the most successful by any officer as it is during this time that Al-Qaeda's plan to bomb the American embassy in Kampala was thwarted. It was also a time when bombings were rampant within the capital Kampala, and once again Tumukunde formed several intelligence committees within the city and the problem was managed. Tumukunde also built an amicable rapport with the Muslim community, which many had accused of spearheading the attacks, so much so that key intelligence information was forwarded to him with ease. Arguably, it was during his term that the Ugandan intelligence apparatus was at its most efficient. Tumukunde was then promoted to the rank of brigadier general and transferred to command the UPDF Fourth Division based in Gulu. At the time, the war with the LRA was ongoing and Tumukunde made significant headway during his time as Division Commanding Officer in diminishing the threat of the Lords Resistance Army. He later played a role in initiating the peace negotiations process with the rebels and also directed the army's efforts in containing the Ebola virus epidemic which had hit the Northern Uganda region at the time. In 2000, Tumukunde was appointed as the director general of the Internal Security Organisation, Uganda's domestic intelligence agency. During his time at ISO, Tumukunde set up structures that returned the agency to being the country's foremost intelligence gathering body, just as he had done with CMI. The Internal Security Organisation became renowned for its efficient and effective approach towards intelligence and counter-terrorism. The fallout Tumukunde's fast rise to the upper echelons of both the political and military scene in Uganda marked him out as one of Uganda's most popular and well-known figures and ultimately, this, alongside his very strong minded and unrelenting dedication to his country, brought him into the sights of the very institutions he helped to consolidate. At a political retreat in 2003, Tumukunde, in the presence of the President and his cabinet, argued against the impending removal of term limits that would give President