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Fighting back against the Vietnamese: 1979–1989

In July 1979, Pol Pot established a new headquarters, Office 131, on the western flank of Mount Thom. He dropped the name "Pol Pot" and began calling himself "Phem". In September 1979, Khieu announced that the Khmer Rouge was establishing a new united front, the Patriotic Democratic Front, bringing together all Cambodians who opposed the Vietnamese occupation. Senior Khmer Rouge members began disavowing the cause of socialism. The group members stopped wearing uniform black outfits; Pol Pot himself started wearing jungle green fatigues and later Thai-made safari suits. Short believed that these changes reflected a genuine ideological shift in the Khmer Rouge. In October, Pol Pot ordered an end to executions, a command which was largely followed. In November 1979, the United Nations General Assembly voted to recognise the Khmer Rouge delegation, rather than that of the Vietnamese-backed government, as the legitimate government of Cambodia. In December, Samphan replaced Pol Pot as prime minister of Democratic Kampuchea, a move that allowed Pol Pot to focus on the war effort and which was perhaps also designed to improve the Khmer Rouge's image.

During the monsoons of summer 1979, the Khmer Rouge troops began filtering back into Cambodia. Many young Cambodians joined the Khmer Rouge forces, wanting to drive the Vietnamese Army out. Boosted by the new Chinese supplies, the Khmer Rouge rebuilt its military structure in early 1980. By mid-1980, the Khmer Rouge claimed it had 40,000 troops active in Cambodia. From 1981, Pol Pot's main goal was to attract popular support among the Cambodian population, believing that this would be vital in enabling him to win the war. In August 1981, he travelled, via Bangkok, to Beijing, where he met with Deng and Zhao Ziyang. Deng had been pushing for Sihanouk, living in Pyongyang, to become Cambodian head of state, something the monarch had reluctantly agreed to in February 1981. In September, Sihanouk, Samphan, and Son Sann issued a joint statement in Singapore announcing the formation of their own coalition government.

I am old now and handicapped. I know that people inside Cambodia fear me. So when we drive out the contemptible Vietnamese and gain peace, I will retire if the comrades so desire. But if I return now, and the comrades can't drive out the Vietnamese, how can I sit still? I must share my experience and knowledge. If the Vietnamese leave and we can defend our country, I will... retire. And when I die I will die peacefully.

— Pol Pot, 1987

In December 1981, Pol Pot and Nuon Chea decided to dissolve the Communist Party of Kampuchea, a decision taken with very little discussion among the party's membership, some of whom were shocked. Many outside commentators believed the dissolution was a ruse, and that the CPK was actually going underground once more, although Short noted that this was not the case. Pol Pot proposed a new Movement of Nationalists that would replace the party, although this failed to fully materialise. The CPK Standing Committee was replaced by a Military Directorate, the focus of which was on driving out the Vietnamese. Pol Pot's decision to disband the party was informed by global events; his anti-Vietnamese army was backed by many capitalist countries while the Vietnamese were backed by most Marxist-governed countries. At the same time, he believed that his main Marxist backers, the Chinese, were themselves restoring capitalism with Deng's reforms. Reflecting the ideological shift, among the Khmer Rouge, collective eating was ended, the ban on individual possessions was lifted, and children were again allowed to live with their parents. Pol Pot commented that his previous administration had been too left-wing and claimed that it had made mistakes because he had placed too much trust in treacherous individuals around him.

In June 1982, at an event in Kuala Lumpur, the Khmer Rouge were among the factions declaring the formation of a Coalition Government of Democratic Kampuchea (CGDK) as an alternative to the administration in Phnom Penh. On the ground in Cambodia there nevertheless remained little military collaboration between these factions, which included the Khmer Rouge as well as the Sihanoukist National Army and Son Senn's Khmer People's National Liberation Front. In 1983, Pol Pot travelled to Bangkok for a medical check-up; there he was diagnosed with Hodgkin's disease. In mid-1984, Office 131 was moved to a new base further into Cambodia, near the O'Suosadey river. In December, the Vietnamese Army launched a major offensive, overrunning the Khmer Rouge's Cambodian base and pushing Pol Pot back into Thailand. There, he established a new base, K-18, several miles outside Trat.

In September 1985, Pol Pot resigned as commander-in-chief of the Khmer Rouge forces in favour of Son Sen; he nevertheless continued to wield significant influence. In the summer he married a young woman named Mea; the following spring their daughter, Sitha, was born. He then travelled to Beijing to undergo cancer treatment at a military hospital, only returning to Cambodia in the summer of 1988. In 1988, the anti-Vietnamese factions entered into negotiations with the Phnom Penh government. Pol Pot deemed this too soon, for he feared that the Khmer Rouge had not gained sufficient popular support to produce significant gains in any post-war election.