It began when Alexander Noble, a dissident Philippine Army colonel linked to the 1989 Philippine coup attempt against President Corazon Aquino, and his supporters, which included Mindanaoan separatists, seized two military garrisons in Cagayan de Oro and Butuan without firing a shot and unilaterally proclaimed the independence of the Federal Republic of Mindanao on October 4, 1990, to be led by a civilian-military junta and with an ultimate goal of removing Aquino from office.

[4] Subsequently reaching the rank of colonel, he served as commander of the 23rd Infantry Battalion in Agusan del Sur from 1980 to 1985, where he organized and trained tribal warriors against the communist New People's Army,[5] and was even baptized as a datu by the Higaonon tribe.

[6] During the presidency of Corazon Aquino, Noble served as deputy commander of the Presidential Security Group (PSG) and helped defend Malacañang Palace during a coup attempt in 1987 launched by the Reform the Armed Forces Movement (RAM) led by Colonel Gringo Honasan.

The latter movement was composed of landowners who opposed Aquino's Comprehensive Agrarian Reform Program and was promised protection by Noble in its plans to declare Mindanao's independence upon the success of the coup.

[9] On his way to Manila to join the coup, he was apprehended at a checkpoint in Santa Rita, Samar but escaped shortly afterwards with the help of sympathetic officers,[10] leaving behind weapons, cash and documents that linked RAM and what Noble referred to as the “Armed Forces of Mindanao”.

[10] After the 1989 coup, RAM devised a new strategy which it called the "enclave concept", in which rebellions would be staged in isolated pockets in the countryside in order to scatter and weaken government resources for a final takeover.

During a Senate hearing, the head of the National Intelligence Coordinating Agency, General Rodolfo Canieso, said that Noble was in charge of the plan, codenamed "Phase III", which was to divide the country by forming a junta in the Visayas and Mindanao.

[10] In Iligan, Lanao del Norte, 100 kilometers west of Cagayan de Oro, about 150 members of an elite army Scout Ranger unit reportedly declared support for Noble but did not become involved in the rebellion.

[13] After realizing that his position was weakening, and following negotiations facilitated bu Misamis Occidental governor Vicente Emano,[14] on October 6, Noble unconditionally surrendered to Senator and former Cagayan de Oro Mayor Aquilino Pimentel Jr. at 3:00 am along with his classmate in the Philippine Military Academy, Colonel Victor Erfe, who was also implicated in previous coup attempts.

[13] Canoy, along with former Cagayan de Oro mayor Constantino Jaraula, was arrested at a hotel and detained inside a small container van at the back of the Misamis Oriental provincial capitol.