At the time of the Japanese invasion of the Malay States in December 1941, John Davis was serving there with the police Special Branch, responsible for intelligence on the Malayan Communist Party (MCP).

In anticipation of a Japanese attack, a plan had been devised by the Oriental Mission, Far Eastern office of the Ministry of Economic  Warfare, to harass the invaders with "stay-behind" parties left in the jungle.

On the day after the surrender of Singapore on February 16, 1942, he and Richard Broome, of the Malayan Civil Service, crossed to Sumatra to seek news of the staybehind parties there.

Japanese activity forced their almost immediate return. Davis, Broome and others were then dispatched by the head of the Oriental Mission in a small vessel to Ceylon (Sri Lanka), where they arrived after 35 days without fresh food and a tiny amount of water

Only a handful of 40 or so Europeans left behind in the Malayan jungle who included Lieutenant-Colonel Freddie Spencer Chapman  avoided capture or death.

Plans were now put in hand to restore contact with the guerrilla forces in Malaya, to trace any survivors of the stay-behind parties and maintain contact by radio and submarine.

Davis, by now commissioned into the 6th Rajputana Rifles, landed from a submarine with a group of Chinese on the coast of the northern state of Kedah in May 1943. Having established these as agents with the local population, he withdrew to Ceylon by the next submarine.

Returning to Malaya by submarine in August 1943, Davis met Chin Peng, nom de guerre of the MCP guerrilla leader operating in Perak, south of Kedah. Chin Peng explained to Davis his opposition to the Japanese occupation and also the extent of the combined guerrilla and civilian organisation, the Anti-Japanese Union and Forces (AJUF) opposing it.

They had heard that a European (whom they guessed was Spencer Chapman) had been training guerrillas in the AJUF camps for two years.