In mid-1985, long-standing tensions within the UNLA –particularly conflicts between Acholi and Langi soldiers– resulted in a series of mutinies and open clashes.

Eventually, an Acholi-led UNLA faction spearheaded by Bazilio Olara-Okello carried out a coup d'état, overthrew President Milton Obote, and installed a new government under Tito Okello.

As the UNLA's military situation declined in the ongoing Ugandan Bush War, with National Resistance Army rebels gaining ground, Obonyo oversaw the move of a large amount of military equipment from the capital Kampala to northern Uganda.

[6] The UNLA ultimately lost the Battle of Kampala, but Obonyo escaped to northern Uganda, specifically Gulu.

Alongside Olara-Okello, he planned for a UNLA military helicopter to attack the ceremony to assassinate the NRA leader and his lieutenants.

Soon after, Obonyo joined other UNLA officers to organize the Uganda People's Democratic Army (UPDA) rebel group in exile, becoming part of its high command.

[10] Obonyo subsequently joined the Lord's Resistance Army in a leadership position to continue his militant opposition,[11] but he was living in peaceful exile in Great Britain by the 2000s.