Around early March 1946, Thomas Morrow, US associate prosecutor of the IPS who was put in charge of investigating Japanese aggression in China, met Thompson and another investigator who was with G-2, the military intelligence division under MacArthur's occupation command. Morrow's request to interview Ishii, who had faked death before being located by MacArthur's intelligence, was turned down.

Then in a memo on June 4, Joseph Keenan, a Harvard graduate who had reportedly been handpicked by President Harry Truman to fill the role of IPS chief counsel, told all his staff at the IPS that a central interrogation center had been established under the control and direction of G-2, headed by Major General Charles A. Willoughby, a die-hard anti-Communist who would become a Cold War warrior. It was merely one month after the start of the Tokyo trial on May 3, 1946.

For those familiar with the entire trajectory of events, this arrangement, which in effect placed any further war crimes investigation under the control of US military intelligence in Tokyo, would be followed, later in trial, by directives from Washington to MacArthur that declared "information obtained from Ishii and associates on BW will be retained in intelligence channels and will not be employed as 'war crime' evidence."

In March 1946, while Morrow was being denied access to Ishii, Thompson was having extensive interviews with the man and his subordinates. In the same Japan Times interview, cited in the 2004 book A Plague Upon Humanity: The Hidden History of Japan's Biological Warfare Program by Daniel Barenblatt, Ishii's daughter Harumi recalled that Thompson "said he had come as an emissary for President Truman" and "literally begged my father for top-secret data on the germ weapons". (The Chinese translation of Barenblatt's book was published in 2016.)