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Peace talks with Moro and communist insurgencies

President Aquino conducted peace talks with the Moro National Liberation Front (MNLF), an armed Moro Muslim insurgency group that sought to establish an independent Moro state within Mindanao. Aquino met with MNLF leader Nur Misuari and various MNLF groups in Sulu. In 1989, the Autonomous Region in Muslim Mindanao (ARMM) was created under Republic Act No. 6734 or the ARMM Organic Act, which established the Moro majority areas in the Mindanao island group as an autonomous region with its own government. The Autonomous Region in Muslim Mindanao lasted from 1989 to 2019, after which it was succeeded by the Bangsamoro Autonomous Region in Muslim Mindanao (BARMM).

The establishment of the Autonomous Region in Muslim Mindanao was opposed by the Moro Islamic Liberation Front (MILF), a militant splinter group from the MNLF that sought to secede from the Philippines to establish an Islamic state in Mindanao. Peace talks with MILF began in 1997 under President Fidel Ramos and violent insurgency officially continued until 2014, when peace accords were formally signed between MILF and the administration of President Benigno Aquino III that would lead to the creation of the BARMM.

The establishment of the ARMM also led to the establishment of Abu Sayyaf, a terrorist group founded in 1989 by Abdurajak Abubakar Janjalani and composed of radical former members of the MNLF. Terrorist attacks by Abu Sayyaf would start in 1995 and continue to the present day, including the 2004 bombing of the MV Superferry 14 that resulted in the deaths of 116 people.

Shortly after becoming president, Aquino ordered the release of hundreds of political prisoners imprisoned during the Marcos era, including communist insurgents belonging to the Communist Party of the Philippines. These releases included leaders such as Communist Party of the Philippines founder Jose Maria Sison and New People's Army founder Bernabe Buscayno, which the military strongly resisted. Preliminary peace talks with the CPP ended after the Mendiola Massacre on January 22, 1987, during which at least 12 farmers were killed at a protest rally.