The FMG launched "police measures" to annex the Eastern Region on 6 July 1967. The FMG's initial efforts were unsuccessful; the Biafrans successfully launched their own offensive, occupying areas in the Mid-Western Region in August 1967. By October 1967, the FMG had regained the land after intense fighting.[9][14] In September 1968, the federal army planned what Gowon described as the "final offensive". Initially the final offensive was neutralised by Biafran troops. In the latter stages, a Southern FMG offensive managed to break through the fierce resistance.[9]

During the war there were great shortages of food and medicine throughout Biafra, due largely to the Nigerian government's blockade of the region. Many volunteer bodies organised the Biafran airlift which provided blockade-breaking relief flights into Biafra, carrying food and medicines in, and later provided means of evacuation for refugee children. On 30 June 1969, the Nigerian government banned all Red Cross aid to Biafra; two weeks later it allowed medical supplies through the front line, but restricted food supplies.[14] Later in October 1969, Ojukwu appealed to the United Nations to mediate a cease-fire. The federal government called for Biafra's surrender. In December, the FMG managed to cut Biafra in half, primarily by the efforts of 3 Marine Commando Division of the Nigerian Army, led by then Colonel Benjamin Adekunle, popularly called "The Black Scorpion", and later by Olusegun Obasanjo. Ojukwu fled to Côte d'Ivoire, leaving his chief of staff, Philip Effiong, to act as the "officer administering the government". Effiong called for a cease-fire 12 January and submitted to the FMG.[9] More than one million people had died in battle or from starvation.[15][16] Biafra was reabsorbed into Nigeria on 15 January.