On 9 March 1942 Governor-General Tjarda van Starkenborgh Stachouwer and head of the Royal Netherlands East Indies Army General Hein ter Poorten capitulated to the Empire of Japan, which had invaded the Indies the month before.
As a result, the Indies fell under Japanese control.
The Japanese banned all forms of organisations, and the MIAI was disbanded in May. It was reformed on 5 September 1942 following a meeting of 30 ulamas in the Des Indes Hotel in Jakarta, and was recognised by the occupation government as the sole Islamic organisation in the country.
At the end of 1943, the organisation was renamed the Council of Indonesian Muslim Associations (Partai Majelis Syura Muslimin Indonesia, or Masyumi).
Fakih was made a member of the Japanese-sponsored advisory board, or Syu Sangi In, for Surabaya.
He held this position until the end of the occupation, concurrently serving on the Masyumi board.

After the atomic bombings of Hiroshima and Nagasaki and the proclamation of Indonesian independence in August 1945, the Japanese began withdrawing from the nascent republic.
The Indonesian republican government, based in Jakarta and including Sukarno as president and Mohammad Hatta as vice president, began to take over infrastructure from the departing Japanese.
By September 1945, however, allied British and Dutch forces had begun to enter the archipelago, hoping to reestablish the status quo ante.
The British initially focused on Java and Sumatra and attempted to avoid armed confrontations with the Republican forces; the Dutch, meanwhile, spent the first months after the Japanese surrender reclaiming the eastern islands with help from Australia.

Fakih, who had begun making contacts within the republican government, participated in the Indonesian Islamic Conference (Muktamar Islam Indonesia) in Yogyakarta from 7 to 8 November 1945.
As a result of these talks, Masyumi was made into a political party representing Islamic interests.
Although Fakih returned to Gresik after the conference, he and his family soon evacuated to Malang due to the outbreak of a battle at Surabaya between Republican soldiers and British forces tasked with repatriating Dutch prisoners of war.

In Malang, Fakih worked with Masjkur and Zainul Arifin to start an armed resistance to fight in the revolution against the returning Europeans.
He served as deputy chief in command of this resistance, which consisted of the Japanese-trained Islamic units Sabilillah and Hizbullah.
After the Dutch launched Operation Kraai in December 1948, Fakih and his family escaped to Surakarta, where he again became active in Muhammadiyah.
Fakih, serving as deputy chair under Bagus Hadikusumo, frequently commuted between Surakarta and the organisation's head office in Yogyakarta.
On 9 March 1942 Governor-General Tjarda van Starkenborgh Stachouwer and head of the Royal Netherlands East Indies Army General Hein ter Poorten capitulated to the Empire of Japan, which had invaded the Indies the month before. As a result, the Indies fell under Japanese control. The Japanese banned all forms of organisations, and the MIAI was disbanded in May. It was reformed on 5 September 1942 following a meeting of 30 ulamas in the Des Indes Hotel in Jakarta, and was recognised by the occupation government as the sole Islamic organisation in the country. At the end of 1943, the organisation was renamed the Council of Indonesian Muslim Associations (Partai Majelis Syura Muslimin Indonesia, or Masyumi). Fakih was made a member of the Japanese-sponsored advisory board, or Syu Sangi In, for Surabaya. He held this position until the end of the occupation, concurrently serving on the Masyumi board.
After the atomic bombings of Hiroshima and Nagasaki and the proclamation of Indonesian independence in August 1945, the Japanese began withdrawing from the nascent republic. The Indonesian republican government, based in Jakarta and including Sukarno as president and Mohammad Hatta as vice president, began to take over infrastructure from the departing Japanese. By September 1945, however, allied British and Dutch forces had begun to enter the archipelago, hoping to reestablish the status quo ante. The British initially focused on Java and Sumatra and attempted to avoid armed confrontations with the Republican forces; the Dutch, meanwhile, spent the first months after the Japanese surrender reclaiming the eastern islands with help from Australia.
Fakih, who had begun making contacts within the republican government, participated in the Indonesian Islamic Conference (Muktamar Islam Indonesia) in Yogyakarta from 7 to 8 November 1945. As a result of these talks, Masyumi was made into a political party representing Islamic interests. Although Fakih returned to Gresik after the conference, he and his family soon evacuated to Malang due to the outbreak of a battle at Surabaya between Republican soldiers and British forces tasked with repatriating Dutch prisoners of war.
In Malang, Fakih worked with Masjkur and Zainul Arifin to start an armed resistance to fight in the revolution against the returning Europeans. He served as deputy chief in command of this resistance, which consisted of the Japanese-trained Islamic units Sabilillah and Hizbullah. After the Dutch launched Operation Kraai in December 1948, Fakih and his family escaped to Surakarta, where he again became active in Muhammadiyah. Fakih, serving as deputy chair under Bagus Hadikusumo, frequently commuted between Surakarta and the organisation's head office in Yogyakarta.
Fakih Usman