In that same time-frame, a growing nationalism was taking place in Sarawak, with people meeting to form an independent Sarawakese language (Bahasa Sarawak), a national dialect of Malay that would have same status as Bahasa Indonesia and Bahasa Malaysia.
The Indonesian government stated its support of the Sarawakese nationalists. Abang Muhammad Salahuddin, the state governor of Sarawak called for help from the Malaysian Armed Forces to put down the nationalist movements. The nationalist movements were fueled by a mix of Iban and Malay nationalists who sought to restore the Kingdom of Sarawak, only in a non-monarchical form.
Armed conflicts ensued in December of 2008, with Malaysian forces crushing poorly-armed Sarawakese militants. With the escalation of the Second Malaysia-Indonesia Border Conflict, the Indonesians put much of their focus on Sarawak, paying little to no attention to Sabah, though pockets of Indonesian soldiers were deployed in Sabah.
Brunei declared and demanded neutrality throughout the war. A conference was held in Manila, brokered by the Philippines for a neutrality pact signed by the governments of Brunei, Malaysia, Philippines and Indonesia which promised Brunei neutrality should armed conflict escalate.
The Isabela City Skirmish forced the Philippines to enter the war, as evidence pointed towards Malaysian activity in the southern Philippines. The Filipino government also used the war as an opportunity to take Sabah by force. Indonesian military leaders made a state visit to Manila to express their approval of Philippine support, as well as their support of the Philippine desire to take Sabah. The Philippine government also expressed a desire to share a land border with Indonesia in Borneo. This had created a two-front war for Malaysia.
In Western Sarawak, pro-Malaysian militants fought the nationalists, and the Indonesian-Philippine coalition. The Malaysian army issued an emergency order, evacuating politicians from Sabah and Sarawak and established military leaders, declaring martial law in both states.
In 2012, the war ended with a United Nations Resolution. Most of Sarawak was carved into an independent state, while territories to the northwest of the Rajang River remained a Malaysian state. Sabah was given to the Philippines, and Indonesia was given land that Malaysian forces had seized prior.
The war had established a land border between Indonesia and Philippines in Borneo, giving the Philippines parts of Borneo.