The 15 January 1966 coup — in which five Majors led by Chukwuma Nzeogwu killed Tafawa Balewa, Sir Ahmadu Bello, Samuel Ladoke Akintola and Festus Okotie-Eboh but spared the Eastern political leadership — was perceived in the North as an Igbo coup. The Unification Decree No. 34 of 24 May 1966, by which General Aguiyi-Ironsi abolished the Federation and merged the regional public services, was read in the Northern Region as confirmation that the conspiracy was structural.
The first wave of pogroms broke at Kano, Kaduna, Zaria, Jos and Sokoto on 29 May 1966: an estimated 600 Igbo civilians were killed in three days. Aguiyi-Ironsi did not punish the perpetrators, did not visit the North, and did not rescind Decree 34. On 29 July 1966 the Northern-led 'counter-coup' assassinated Aguiyi-Ironsi at Government House Ibadan and brought General Yakubu Gowon to power; in the subsequent purge, an estimated 200 Eastern officers and men were killed at Ikeja, Kaduna and Abeokuta barracks.
The second and decisive wave came on 29 September 1966 — the so-called 'Massacre of 29 September' — when coordinated mob attacks across Sabon Gari quarters of Kano, Kaduna, Zaria, Jos, Maiduguri, Sokoto and Gusau killed between 8,000 and 30,000 Easterners over three days. The pattern was identical at each location: the Army stood aside, the Police facilitated, and the killings were carried out by gangs led by serving NCOs and local political activists. Approximately 1.5 million Easterners fled to the East in a refugee movement comparable in scale to the 1947 Partition of India. No prosecutions ever took place.
Lt-Col Emeka Ojukwu, Military Governor of the Eastern Region, presented the casualty figures at the Aburi Conference (4–5 January 1967) in Ghana, demanding regional autonomy and the prosecution of identified killers. Gowon's repudiation of the Aburi Accord — and his unilateral creation of twelve states on 27 May 1967, which split the East and isolated Igbo-land — produced the Eastern Consultative Assembly's vote for secession on 30 May 1967. The 1966 pogroms are the unbroken origin-code of every subsequent south-east crisis: MASSOB (1999), IPOB (2012), the Eastern Security Network (2020), and the Unknown Gunmen attacks (2021-).