The coup of January 1966 had an ethnocentric cast that aroused the suspicions of Northerners. In addition, failure by Major General Johnson Aguiyi-Ironsi to meet Northern demands for the prosecution of the coup plotters further inflamed Northern anger. Then came Ironsi's Decree Number 34, which proposed the abolition of the federal system of government in favor of a unitary state, a position which had long been championed by the Southern parties - the NCNC and the AG. On 29 July 1966, Ironsi was killed. A seperate coup led by Lieutenant Colonel Murtala Mohammed then seized the Ikeja airport in Lagos. Several Igbo and Eastern minority officers were killed during the counter-coup.

The original intention of Murtala Mohammed and his fellow coup-plotters seems to have been to engineer the secession of the Northern region from Nigeria as a whole, but they were subsequently dissuaded of their plans by several advisors when the economic difficulties of a potential Northern Nigerian State were pointed out to him by civil servants and British diplomats. The young officers then decided to name Lieutenant Colonel Gowon, who apparently had not been actively involved in events until that point, as Nigerian Head of State. Gowon's unique background as a Christian Northerner made him the right choice in a period of ethnic tension. On ascent to power Gowon reversed Ironsi's abrogation of the federal principle.

In the meantime, the July Counter-Coup had unleashed terror against the Igbos throughout the Northern Region. Hundreds of Igbo officers were murdered during the revolt. Soon Northern civilians joined in. Tens of thousands of Igbos were killed throughout the North. The persecution precipitated the flight of more than a million Igbo's towards their ancestral homelands in eastern Nigeria. Lieutenant Colonel Chukwuemeka Odumegwu Ojukwu, the military governor of the Eastern region who did not allow attempts by Northern soldiers stationed in his region to replicate the massacres of Igbo officers, argued that if Igbo lives could not be preserved by the Nigerian state, then the Igbos reserved the right to establish a state of their own in which their rights would indeed be respected.

There arose tension between the Eastern region and the northern controlled federal government lead by Gowon. On 4-5 January 1967, in line with Ojukwu's demand to on meet for talks only on neutral soil, a summit attended by Gowon, Ojukwu and other members of the Supreme Military Council was held at Aburi in Ghana, the stated purpose of which was to resolve all outstanding conflicts and establish Nigeria as a confederation of regions. The outcome of this summit was the Aburi Accord. The Aburi Accord did not see the light of the day, as in a move to check the influence of Ojukwu's government in the East, Gowon announced on 5 May 1967 the division of the 3 Nigerian regions into 12 states. This resulted in the division of Ojukwu's Eastern Region into 3 states (Rivers State, South-Eastern State, and East-Central State). The non-Igbo South-Eastern and Rivers states which had the oil reserves and access to the sea, were carved out to isolate the igbo areas as East-Central state.

On 30 May 1967, Ojukwu responded to Gowon's announcement by declaring the formal secession of the Eastern Region, which was to be known as the Republic of Biafra (See the maps section of the application to view the region called Biafra). This was to trigger a war that would last some 30 months, and see the deaths of more than 100,000 soldiers and over a million civilians, most of the latter died of starvation. The end of the war came about on 13 January 1970, with Colonel Olusegun Obasanjo's acceptance of the surrender of Biafran forces.