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It was fought between Malaysia and a loose coalition of countries and groups that included Indonesia, Philippines and the proclaimed independent State of Sarawak.
Through late 2008, disputes between Indonesia and Malaysia had culminated into anti-Malaysia sentiments in Indonesia, and vice versa. In that same time-frame, the citizens in Sarawak had begun to express a mutual animosity for Malaysia. On November 12, 2008 as a result of the Indonesia border skirmish blamed on Malaysian soldiers, Indonesia declared war on Malaysia and military hostilities sky-rocketed.
Brunei and Philippines declared a neutral stance, and a meeting was held in Manila in which Malaysian prime minister Abdullah Ahmad Badawi, Brunei's sultan Hassanal Bolkiah, Indonesian president Susilo Bambang Yudhoyono and Philippine president Glorya Mcapagal-Arroyo signed a Neutrality Pact, promising not to involve Brunei or Philippines.
However, the Philippines was forced to enter the war after the Isabela City skirmish, was was blamed heavily on Malaysian troops masquerading as Bangsamoro nationalists in the southern Philippines. The Philippines formally declared war on Malaysia on November 25, 2008, opening up a Sulu Front of the war. Although the Philippines originally intended to independently enter the war with no correlation or connection to Indonesia's cause, and as a retaliation against Malaysia, it later joined and formed a loose coalition with Indonesia and revolutionary militants in Sarawak. Philippines also re-focused their intent on taking Sabah by force, aiding the Indonesians in Sarawak and in return, the Indonesian military aided the Filipinos in Sabah.
At the war's end, Malaysia experienced huge territorial losses. The northern and eastern parts of Sabah were given to the Philippines, parts of southern Sabah given to Indonesia while western Sabah remained Malaysian territory.
Sarawak was given independence, but the lands west of the Rajang River remained Malaysian territory.
The territorial changes had also created a physical land border between Indonesia and the Philippines, the Philippines became the fourth country to share Borneo.