In the 1930s, Lim Bo Seng, under the alias Tan Choon Lim, participated in anti-Japanese activities in Singapore, particularly in supporting the China Relief Fund and also in activities organised by the Nanyang Federation to boycott Japanese goods. Upon the request of Sir Shenton Thomas, the Governor, he formed the Chinese Liason Committee to assist in civil defence. With the fall of Kota Bahru in Malaya in 1942, he, as the head of the Labour Services of the Overseas Chinese Mobilization Council, and Tan Kah Kee organised more than 10,000 men for the British Government to man essential services and to construct defences around the island. As the Japanese troops travelled to Singapore, his men helped dynamite the Causeway.

On 11 February, he left Singapore and travelled to Sumatra with other Chinese community leaders and made his way to India later. He joined the British resistance group, Force 136, and was trained by the British for intelligence work. He then recruited and trained hundreds of secret agents through intensive military intelligence missions from China and India. Force 136 was a special operations force formed by the British and the Chinese governments in June 1942 to support resistance groups behind enemy lines and to coordinate guerilla operations in support of the eventual British invasion of Malaya.
In May 1943, he sent the first batch of Force 136 agents to Malaya to conduct the operation codenamed Gustavus. The operation aims to establish an espionage network in Malaya and Singapore to gather military intelligence about the Japanese forces to aid the British in planning their re-capture of the colonies from the Japanese, codenamed Operation Zipper. It was set up in the urban areas in Pangkor, Lumut, Tapah and Ipoh. One of the Chinese provision shops in Ipoh, Jian Yik Jan, was used as an Allied espionage base. Communications between the agents were done by smuggling messages in empty toothpaste tubes, salted fish and diaries. Lim arrived in Malaya in November 1943 and used the alias Tan Choon Lim to avoid identification by the Japanese, claiming to be a businessman when he passed through checkpoints.

Operation Gustavus failed before the agents managed to achieve any results. An unknown communist guerrilla was captured by the Japanese in January 1944 and they revealed the existence of the Allied spy network operating on Pangkor Island. The Japanese launched a full-scale counter espionage operation on the island and by late March 1944, more than 200 Japanese soldiers had landed on Pangkor Island.

On March 24, the Japanese Kempeitai arrested a fisherman, Chua Koon Eng, at Teluk Murrek on the Perak coast. He was working on Pangkor Island when Li Han Kwang of Force 136 approached him and requested to use his boat for their communications. He also told the Kempeitai what he knew when the Kempeitai threatened to kill civilians. Li Han Kwang was later captured by the Japanese and he confirmed Chua's accounts of Force 136 under torture and then began to feign cooperation with the Japanese in order to escape captivity.

Lim Bo Seng was captured by the Japanese under Marshal Onishi Satoru at a roadblock in Gopeng the next day. He was taken to the Kempeitai headquarters for interrogation but he refused to provide the Japanese with any information about Force 136 despite being subjected to severe torture. Instead, he protested against the ill-treatment of his comrades in prison. He fell ill with dysentery and was bedridden by the end of May 1944. He died in the early hours on June 29, 1944. He was later buried behind the Batu Gajah prison compound in an unmarked spot.