The personal papers of the neurophysiologist John C. Lilly at Stanford University hold a classified paper he wrote in the late 1950s on the behavioural modification and control of ‘human agents’. The paper provides an unnerving prognosis of the future application of Lilly’s research, then being carried out at the National Institute of Mental Health. Lilly claimed that the use of sensory isolation, electrostimulation of the brain, and the recording and mapping of brain activity could be used to gain ‘push-button’ control over motivation and behaviour. This research, wrote Lilly, could eventually lead to ‘master-slave controls directly of one brain over another’. The paper is an explicit example of Lilly’s preparedness to align his research towards Cold War military aims. It is not, however, the research for which Lilly is best known. During the 1960s and 1970s, Lilly developed cult status as a far-out guru of consciousness exploration, promoting the use of psychedelics and sensory isolation tanks. Lilly argued that, rather than being used as tools of brainwashing, these techniques could be employed by the individual to regain control of their own mind and retain a sense of agency over their thoughts and actions. This article examines the scientific, intellectual, and cultural relationship between the sciences of brainwashing and psychedelic mind alteration. Through an analysis of Lilly’s autobiographical writings, I also show how paranoid ideas about brainwashing and mind control provide an important lens for understanding the trajectory of Lilly’s research.