The album begins with the protagonist, Nikki, in a hospital. He lies in a near catatonic state, unable to remember anything but snippets from his past. Suddenly, Nikki's memories come flooding back in a torrent. He remembers how, as a heroin addict and would-be political radical frustrated with contemporary society due to the economic inequality, corruption, and hypocrisy around him, he was manipulated into joining a supposed secret organization dedicated to revolution. At the head of this organization is a mysterious political and religious demagogue known only as Dr. X, who manipulates Nikki through a combination of his heroin addiction and brainwashing techniques to become an assassin.

Whenever Dr. X uses the word "mindcrime", Nikki becomes his docile puppet, a state which Dr. X uses to command Nikki to undertake any murder that the Doctor wishes. Through one of Dr. X's probable associates, a corrupt priest named Father William, Nikki is offered the services of a prostitute-turned-nun named Sister Mary. Through his friendship and growing affection toward Sister Mary, Nikki begins to question the nature of what he is doing, seeing that Dr. X has his own nefarious agenda. Dr. X takes notice and, seeing a potential threat in Mary to his cult of personality, orders Nikki to kill both her and the priest. Nikki goes to Mary's church and kills the priest, but, after confronting Mary, he fails to comply with the command to murder her. He and Mary decide to leave the organization together, and Nikki goes to Dr. X to tell him that they are out. Dr. X, however, reminds Nikki that he is an addict, and that he is the one who can provide him with his daily fix. Nikki leaves, conflicted and uncertain, and he returns to Mary only to find her dead.