In the 1943-1944 Pontianak incident, the Japanese orchestrated a mass arrest of Chinese, Malay elites, Javanese, Menadonese, Dayaks, Bugis, Bataks, and Minangkabau in Kalimantan, including all of the Malay Sultans, accused them of plotting to overthrow Japanese rule, and then massacred them. The Japanese falsely claimed that all of those ethnic groups, and organisations such as the Islamic Pemuda Muhammadijah, were involved in a plot to overthrow the Japanese and create a "People's Republic of West Borneo". The Japanese claimed that, "Sultans, Chinese, Indonesian government officials, Indians and Arabs, who had been antagonistic to each other, joined together to massacre Japanese", naming the Sultan of the Pontianak Sultanate as one of the "ringleaders" in the planned rebellion. Up to 25 aristocrats, relatives of the Sultan of Pontianak, and many other prominent individuals were named as participants in the plot by the Japanese and then executed at Mandor. The Sultans of Pontianak, Sambas, Ketapang, Soekadana, Simpang, Koeboe, Ngabang, Sanggau, Sekadau, Tajan, Sintang, and Mempawa were all executed by the Japanese; respectively, their names were Sjarif Mohamed Alkadri, Mohamad Ibrahim Tsafidedin, Goesti Saoenan, Tengkoe Idris, Goesti Mesir, Sjarif Saleh, Goesti Abdoel Hamid, Ade Mohamad Arif, Goesti Mohamad Kelip, Goesti Djapar, Raden Abdul Bahri Danoe Perdana, and Mohammed Ahoufiek. They are known as the "12 Dokoh". In Java, the Japanese jailedSyarif Abdul Hamid Alqadrie, the son of Sultan Syarif Mohamad Alkadrie. Since he was in Java during the executions Hamid II was the only male in his family not killed, while the Japanese beheaded all 28 other male relatives of Pontianak Sultan Mohammed Alkadri. Among the 29 people of the Sultan of Pontianak's family who were beheaded by the Japanese was the heir to the Pontianak throne. Later in 1944, the Dayaks assassinated a Japanese named Nakatani, who was involved in the incident and who was known for his cruelty. Sultan of Pontianak Mohamed Alkadri's fourth son, Pengeran Agoen, and another son, Pengeran Adipati, were both beheaded by the Japanese in a public execution. The Japanese extermination of the Malay elite of Pontianak paved the way for a new Dayak elite to arise in its place. According to Mary F. Somers Heidhues, during May and June 1945, some Japanese were killed in a rebellion by the Dayaks in Sanggau. According to Jamie S. Davidson, this rebellion, during which many Dayaks and Japanese were killed, occurred from April through August 1945, and was called the "Majang Desa War". The Pontianak Incidents, or Affairs, are divided into two Pontianak incidents by scholars, variously categorised according to mass killings and arrests, which occurred in several stages on different dates. The Pontianak incident negatively impacted the Chinese community in Kalimantan.
