Shortly afterwards he was elected President of the Haripura Congress Session in 1938. During his term as Congress President, he talked of planning in concrete terms, and set up a National planning Committee in October that year. At the end of his first term, the presidential election to the Tripuri Congress session took place early 1939. Subhas Chandra Bose was re-elected, defeating Dr. Pattabhi Sitaramayya who had been backed by Mahatma Gandhi and the Congress Working Committee. Clouds of World War II were on the horizon and he brought a resolution to give the British six months to hand India over to the Indians, failing which there would be a revolt. There was much opposition to his rigid stand, and he resigned from the post of president and formed a progressive group known as the Forward Block.

Subhas Chandra Bose now started a mass movement against utilizing Indian resources and men for the great war. There was a tremendous response to his call and he was put under house arrest in Calcutta. In January 1941, Subhas Chandra Bose disappeared from his home in Calcutta and reached Germany via Afghanistan. Working on the maxim that "an enemy's enemy is a friend", he sought cooperation of Germany and Japan against British Empire. In January 1942, he began his regular broadcasts from Radio Berlin, which aroused tremendous enthusiasm in India. In July 1943, he arrived in Singapore from Germany. In Singapore he took over the reins of the Indian Independence Movement in East Asia from Rash Behari Bose and organised the Azad Hind Fauj (Indian National Army) comprising mainly of Indian prisoners of war. He was hailed as Netaji by the Army as well as by the Indian civilian population in East Asia. Azad Hind Fauj proceeded towards India to liberate it from British rule. Enroute it lliberated Andeman and Nicobar Islands. The I.N.A. Head quarters was shifted to Rangoon in January 1944. Azad Hind Fauj crossed the Burma Border, and stood on Indian soil on March 18,1944.