Gowon's lack of talent for tactics and strategy came to the fore when the Uganda–Tanzania War broke out in 1978, and his leadership of the Uganda Army during this conflict was extensively criticised.

When the new Ugandan government of Yoweri Museveni offered him to return to his home country in 1994, he accepted and founded a nonprofit organization to help ex-combatants find civilian jobs.

The trial generated much publicity and was controversial, as some regarded it as important chance to finally address the crimes of Amin's dictatorship, while others claimed that it was politically motivated.

In order to secure the power over the Uganda Army, both launched extensive recruitment drives to enlist as many members of their own respective tribal groups as possible.

Another Ugandan ex-officer later commented that Gowon was not prepared for such a promotion, and was just appointed because he belonged to Amin's own tribal group and religion.

With the President as his personal patron, Gowon held great power over the Simba Battalion, probably more than the official commanding officer, Colonel Ali Fadhul.

Despite his inexperience, Gowon won some respect as second-in-command of the Simba Battalion, and was regarded as more polite and humane than other military officers who abused their power.

While he was stationed at Mbarara, the Simba Battalion carried out numerous massacres of Acholi and Langi; Gowon later claimed that he knew nothing of any mass murders.

[20] As Colonel Fadhul went missing amid the attack's early stages, Gowon was left in command of the Simba Battalion, and organized a counter-attack against a rebel column of 350 fighters.

[22][21] It is known that the commander had good connections to at least some members of the State Research Bureau, Amin's secret police organisation, and some victims of the purges as well as their families believe that Gowon ordered their deaths.

[27][d] He was placed under house arrest, but Army Chief of Staff Mustafa Adrisi intervened on his behalf, allowing Gowon to be flown to Libya for medical treatment of a stomach ailment.

Gowon's appointment was mostly owed to the fact that he was regarded as loyal to Amin, and lacked a power base in the military to threaten the President.

[32][26][45] Although Gowon had thus risen to one of Amin's closest allies and proven to be competent in politics, he was not qualified as head of the military, and lacked training in basic strategy.

[34][46] In September 1978 Amin, in response to international criticisms of his regime, announced the creation of a human rights committee "charged with the duty of explaining Uganda's position abroad".

The Tanzanian border guards were overwhelmed and the Kagera salient occupied, whereupon the Ugandan troops launched a spree of plundering, rape, and murder.

[e] After the Uganda Army blew up a bridge across the Kagera river, Gowon believed that he had made a Tanzanian counter-offensive impossible and thereby won the war.

This turned out to be a catastrophic miscalculation, as the Tanzania People's Defence Force (TPDF) counter-attacked using a pontoon bridge, routing the Ugandans.

[42] Thereafter, Tanzania began preparing a counter-invasion of Uganda, but Gowon and other high-ranking commanders ignored warnings by subordinate officers about an impending Tanzanian offensive.

[48] Colonel Bernard Rwehururu in particular accused Gowon of gross incompetence, recalling an occasion when he showed the Chief of Staff a map with possible Tanzanian invasion routes.

[52] Eventually, Amin's Libyan ally Muammar Gaddafi intervened by sending an expeditionary force,[49] whereupon a combined Ugandan-Libyan counter-offensive was launched against Lukaya on 10 March 1979.

[53] According to an unidentified "high Ugandan official" who was in exile in Nairobi at the time, Gowon and other officers unsuccessfully urged Amin to step down as President after the Battle of Lukaya.

His troops believed that he had deserted,[49] prompting one of them to comment in an interview with the Drum magazine that "Our recent chief of staff, Major General Gowon, has disappeared.

[59] Meanwhile, Amin's regime collapsed as the Tanzanians and their Ugandan rebel allies occupied Kampala, prompting most Uganda Army loyalists to flee into Sudan and Zaire.

As many believed that Gowon had actually been bribed by the Tanzanians and lost the war on purpose, he became a persona non grata among the Ugandan exiles and thus excluded from plans by Amin loyalists to launch a rebellion to regain power.

[63] The former Chief of Staff also founded "Good Hope"[65] and "Alternatives to Violence", nonprofit organizations to help ex-combatants to find civilian jobs.

The former Chief of Staff disputed any knowledge of or involvement in Laki's death, but was placed in the Luzira Maximum Security Prison and put on trial.

[25] The prosecutors, the families of victims, and reporters saw Gowon's trial as the last chance to finally address the injustices of Amin's regime which had killed between 100,000 and 300,000 people, as the majority of the perpetrators were already quite old.

[77] In the middle of the trial, defense attorney Caleb Alaka simply disappeared; he later resurfaced in Western Nile, where he had taken a job representing a rebel group which had signed a peace deal with the Ugandan government.

[82] Following his release, Gowon resumed his work in the veterans association, and consequently advocated for a greater unity among ex-combatants of West Nile origin.

[83] By 2005, he was spending most of his time at Arua where he still possessed a house,[84] and had joined a class action lawsuit against several banks that had frozen assets of Amin-era officials worth 50 million dollars.