He found Ishii having a mild argument with Dr. Shinozuka about "Project Black Sun". As the trio discusses the repercussions of the spy trying to sniff out valuable information Ishii orders Shinozuka to complete 'Project Black Sun' which Shinozuka opposes as he declares the procedure isn't ready yet and he needs more time. Ishii, a man of utter discipline and calm composure couldn't bear hearing the last word once again and lost control going full berserk, a sight to behold, Kitano mused to himself.

"I'm the man in charge here, you whimpering pathetic bastard! You will do as I command you to do, no more questioning." Ishii screamed. "Do you have even the slightest idea what is at stake here? The country's future, my future, my reputation! I have a responsibility towards my citizens and my country and I sure as hell won't let some idiot in a lab coat dictate the terms."

Shinozuka was terrified of witnessing such a change in Ishii's behavior on such short notice and lost his marbles for a few seconds before agreeing to Ishii's command. All he could muster to utter was a meek "Yes sir" after the verbose storm had subsided. Ishii leaves the basement along with Kitano while heading towards the interrogation room and gives a final warning to Shinozuka curtly,

"Don't you dare test my patience doctor. See to it that Project Black Sun is completed without any further delay".

As Ishii and Kitano subject Alan through gruelling sessions of interrogation with occasional torture along the way, Alan reveals his true identity as an American spy from the CIA who was sent here to investigate the Togo Unit and its subsequent dealings.

"What is it exactly that you're trying to do here? What is Project Black Sun?" Alan said.