Promoted to rear admiral on 1 May 1943, in September Takagi (due to his access and unique knowledge of classified files from his time as chief of the Research Section) was asked by Navy Minister Shigetarō Shimada to compile a report analyzing Japanese defeats during the Pacific campaign of 1942.

Going far beyond its original purpose, Takagi's analysis of combat evidence, conditions in the Japanese home islands, and air and shipping losses as of that year convinced him that Japan's defeat was inevitable.

Believing the only solution for Japan was the elimination of the Tojo-led government and negotiation of a truce with the United States, Takagi was hesitant to present the report to Shimada, instead beginning planning for the assassination of Prime Minister Hideki Tōjō before his removal from office in July 1944.

As a member of the Navy Staff College's Research Department, Takagi was encouraged by the newly appointed Navy Minister Mitsumasa Yonai to compose an ultrasecret document proposing the most favorable scenario for Japan's eventual withdrawal from the Pacific, a project he continued working on in cooperation with other government officials until Japan's surrender in August 1945.

Rengō kantai shimatsuki [A factual description of the Combined Fleet] by Rear Admiral Sōkichi Takagi (Tokyo: Bungei Shunjūsha, 1949), ASIN: B000Jbjed4 [元海軍少将高木惣吉著, 聯合艦隊始末記 (東京: 文藝春秋社, 1949)]