Susumu Nakoshi, a homeless man living in his car, is approached by a medical student named Manabu Ito, who offers him money to participate in an experimental procedure called trepanation. The procedure involves drilling a hole in the skull to stimulate the brain’s dormant potential, purportedly granting the ability to see beyond ordinary perception. Initially skeptical, Susumu agrees, driven by financial desperation and curiosity. After the surgery, he begins to perceive people and the world in a distorted, surreal manner, seeing grotesque manifestations of their inner psyches, referred to as "homunculi." These visions reveal hidden desires, fears, and traumas, often taking on monstrous or symbolic forms.

As Susumu navigates this new reality, he encounters a variety of individuals, each with their own psychological complexities. His interactions with these characters, including a woman with a split personality, a man obsessed with control, and a child with a dark secret, force him to confront his own repressed memories and unresolved trauma. The line between reality and hallucination blurs, as Susumu struggles to determine whether his visions are a product of the procedure or a manifestation of his deteriorating mental state.

The narrative delves deeply into themes of identity, perception, and the human psyche, exploring how individuals construct their sense of self and how trauma shapes behavior. Susumu’s journey becomes increasingly introspective, as he grapples with his own homunculus and the darker aspects of his past. The story’s tension builds as Susumu’s perceptions grow more chaotic, leading to a climactic confrontation with his own inner demons and the consequences of his actions.

"Homunculus" is a psychological thriller that combines elements of horror, mystery, and existential inquiry, presenting a complex and often unsettling exploration of the human mind. The characters are intricately developed, with their psychological struggles serving as the driving force behind the plot. The manga’s narrative structure is nonlinear, frequently shifting between past and present, reality and hallucination, to reflect the fragmented nature of Susumu’s psyche. This approach creates a disorienting yet compelling reading experience, drawing the audience into the protagonist’s unraveling mental state.