Following the killing of General Johnson Thomas Umunnakwe Aguiyi Ironsi in July 1966, Ironsi's chief of army staff, Yakubu Gowon, became head of state and supreme commander of the armed forces. The federal system of government was restored on August 31, 1966, but political dissent continued in the north.

The most virulent violence was in the east where mobs continued to rampage, targeting ethnic Igbo and other tribes.

Gowon responded to the unrest by seeking to limit the regional powerbrokers and splitting Nigeria's four political regions into 12 states. Despite this political effort and the deployment of more troops, the violence did not end. The eastern region's governor and military commander, Colonel Chukwuemeka Odumegwu Ojukwu — an Oxford-educated millionaire's son — blamed Gowon's central government for the failure to bring stability to the area and refused to acknowledge the central government's authority.

Ojukwu's eastern region seceded on May 30, 1967, declaring the independent Republic of Biafra. Gowon's government responded by sending troops to the region. A bloody civil war ensued, lasting for two and a half years and killing as many as a million Nigerians. In the end, Biafra collapsed and Gowon forcibly folded the region back into Nigeria.

Following this victory, Gowon announced that Nigeria would remain under military rule for six more years, promising to return the country to civilian rule in 1976.

"I solemnly repeat our guarantees of a general amnesty for those misled into rebellion. We guarantee the personal safety of everyone who submits to federal authority," he said at the time.

But four years later, Gowon reneged, saying it was infeasible to return to civilian rule. Protests and instability flared throughout the country. On July 29, 1975, Gowon was ousted in a bloodless coup led by Brigadier General Murtala Muhammad.