In 1960s London, British intelligence agent Harry Palmer is assigned to investigate the mysterious disappearance and brainwashing of scientists. Palmer, a former army sergeant with a criminal past, is reluctantly transferred to a counter-espionage unit led by Major Dalby after his previous superior, Colonel Ross, manipulates the situation. Palmer is tasked with locating a missing scientist, Dr. Radcliffe, who was kidnapped and subjected to a psychological conditioning process known as the "IPCRESS" technique. Palmer's investigation leads him through a labyrinth of espionage, revealing a complex web of conspiracies and deceit involving high-ranking officials and foreign agents.

As Palmer delves deeper into the case, he discovers that the brainwashing operation has deeply infiltrated the British intelligence community. His journey becomes increasingly perilous as he contends with double agents, cryptic audiotapes, and conflicting loyalties. With growing suspicion and pressure from his superiors, Palmer must navigate treacherous alliances and avoid numerous traps to uncover the truth. The tension mounts as he unravels the layers of manipulation and betrayal, striving to solve the mystery before it engulfs both him and the country's national security.