Manabu Ito, a rich 22 year old medical student, tows 34 year old Susumu Nakoshi's car in order to convince him to undergo trepanation. Nakoshi is an actuary on an extended vacation who decided to take time off and live inside his car between a park where the homeless reside and a tall affluent hotel he used to frequent. He later hands in his letter of resignation from being an actuary at a life insurance company. Susumu is a misanthrope who does not believe in the supernatural, just the physical reality in front of him. Manabu is a medical student who is interested in human behavior, from the psychological, medical, to even the occult. As Susumu's sixth sense begins to be activated by the trepanation, he begins to confront his own past while at the same time becoming entangled in the lives of others.
- Trepanation: Volume 1
The story starts with Nakoshi sleeping in his car, parked in front of a park. Nakoshi is friends with the homeless community in the park, which is directly across from a classy hotel. Nakoshi is extremely fond of his car, to the point where he has no problem starving if it will provide gasoline for his car. He has become so knowledgeable of the ins and outs of it, that he is able to discern any engine trouble by sound alone. Nakoshi is known to be a pathological liar, but, as he provides alcohol to the denizens of the park, he isn't given any guff for it. Nakoshi feels extremely withdrawn and isolated from the world, he identifies with neither the poor (he regurgitates any food given to him by his homeless friends) nor the rich (he harbors disdain towards them for "looking down on him" from the hotel.)
Ito, a very effeminate man in an extremely gaudy manner, begins spying on, and eventually approaches, Nakoshi. Ito offers a proposition to Nakoshi, to undergo trepanation for 700,000 yen. Ito states that he believes the process will "develop a person's sixth sense". Nakoshi flatly refuses, but eventually accepts the offer after his car is towed away. Ito believes that Nakoshi is the perfect subject because he "lives between two worlds", as his car/home is between the rich (the hotel) and the poor (the park). Ito discusses over dinner his obsession with studying people, and states that trepanation increases blood flow to the brain, and, in theory, should elevate Nakoshi's brain to a higher level. Ito then pays to have Nakoshi's car released, and eventually takes Nakoshi to his private surgical lab, really an apartment his father purchased for him. After the surgery, Nakoshi is a bit skeptical as to the authenticity over his alleged increase in "psychic activity", but is a bit disturbed when he reads that the majority of Ito's patients have either experienced no change, committed suicide or became institutionalized.
Ito then plans a ten day test, to see if Nakoshi has gone under any changes. After a few days of inconclusive results, Ito is a bit disheartened and Nakoshi is all the more certain in his skepticism. He his utterly shocked however, when he closes his right eye only, and sees people around him transformed into bizarre beings, ranging from physically mutated, such as people appearing completely flat, to people appearing as animals, trees, etc. When Nakoshi opens his eye however, he sees people exactly as normal. Nakoshi ends up running afoul of a Yakuza member, who, when Nakoshi closes his eye, appears to be a robot. Nakoshi, however, notices the "robot" has the pinky finger of a child. When Nakoshi states this, the Yakuza is stunned. The Yakuza's form then changes, to where its arm grows into a sickle, and begins cutting his pinky off. Also the face plate opens up to reveal the face of a child. As Nakoshi describes what he's seeing, the Yakuza begins involuntarily crying. Shocked, he lets Nakoshi go.
- Yakuza: Volume 2
Nakoshi is extremely frightened over these newfound "hallucinations" and demands answers from Ito. Nakoshi describes his visions as "people taking the form of monsters". After a bit of studying into the matter, Ito calls Nakoshi and states he has discovered that what he sees are "homunculi". Before Nakoshi can meet up with Ito, however, he is apprehended by the yakuza once again. The yakuza's cronies state that Nakoshi is going to have his pinky removed, as that is what the yakuza is known for. The yakuza demands to know how Nakoshi manipulated him to which Nakoshi has no idea. Nakoshi then observes that with his right eye closed, the Yakuza's robot form even physically feels like a robot to Nakoshi. After further probing, Nakoshi observes the pinky finger of the yakuza's homunculus form is terribly scarred. Nakoshi also discovers that the yakuza is powerless when he grabs his pinky. After Nakoshi detects an odd scent on the homunculus' finger, he says that the yakuza feels guilty for something. After Nakoshi tearfully describes an event in his own childhood, in which a prank he pulled cost his best friend his leg, the yakuza homunculus completely breaks down, and reveals a naked child with a swollen pinky contained within. Nakoshi states that this act was what drove him to isolate himself from people. The yakuza confesses that he accidentally cut off his best friend's pinky finger with a sickle whilst harvesting wheat, and then began removing other people's pinky fingers as a way to subvert his own guilt. The yakuza then relinquishes his life of crime, and severs his own pinky to atone for his crimes. Afterward, Nakoshi simply sees the man as a normal person when he closes his right eye, and he and the man part ways.
- Yukari: Volume 3-6
The next day, Ito meets up with Nakoshi again, and explains the nature of homunculi. Ito states that the homunculus is a physical representation to a person's subconscious mind, and usually reflects a flaw, conflict, or other problem the person may have internally, for example a woman who was choked by her husband appears to Nakoshi as a woman with a stretched neck with finger marks embedded in it. Ito cautions however, that the homunculus reflect not only their own flaws, but also Nakoshi's. Ito is very eager to test out this revelation and begins hopping from location to location with Nakoshi in tow in hopes of discovering all there is to discover in this field. Nakoshi discovers that his homunculus' arm has become a robot, identical to the yakuza's homunculus form. After a few examinations of other people, Nakoshi discovers a new homunculus, in a young underwear display girl, named Yukari. Yukari's homunculus form is that of a "sand monster". Nakoshi then observes that Ito's homunculus is that of sentient liquid in the shape of a man. During a private display session, the Yukari's homunculus begins transforming into many bizarre "sand monsters". Ito then displays a sexual interest in Yukari, and schemes for a way to use her inner flaws to his advantage, with Nakoshi's help. The plan is initially successful, as the two men catch Yukari shoplifting and manipulate her into "dating" Ito. The plan backfires however, as, when Ito and Yukari are alone, she calls Ito a virgin, which causes his homunculus form to sprout leaks, and Ito runs away in panic. As Nakoshi drives Yukari home, he observes that she is not made of sand, but a multitude of tiny "symbols" and words. Nakoshi drops Yukari off and sees Yukari's mother's homunculus is an insect-like monster, that "reassembles" Yukari to her own liking.
Yukari is shown cutting her leg, and Nakoshi looks through Yukari's cellphone, discovering various entries in it, showing her own lack of a self image. Yukari then begins drinking her own blood, while Nakoshi consumes his own semen. After bartering with her cellphone, Nakoshi arranges a meet with Yukari. The meet turns sexual, in which Nakoshi attempts to physically decipher the girl's homunculus. After the sexual encounter begins taking a nightmarish turn, Nakoshi discovers that Yukari's "weak spot" is the leg she cuts. He spreads her blood about, which destroys her sandy symbols, and turns her "human". After his encounter with Yukari, Nakoshi discovers his leg has turned into a mass of sandy symbols, much like what happened to his arm after the yakuza episode.
- Tomida and Ito: Volume 6-8
Several aspects of Nakoshi's past life are described. It is revealed that he was a fabulously wealthy businessman working for the Bank of Manhattan, and prided himself on so many take overs of other companies, but eventually left his job for some unknown reason. Nakoshi was a promiscuous misanthrope, emotionally deadened, and felt nothing for his monetary success. Nakoshi, in present day, remembers that he often saw a man in the park from his hotel, sitting on a bench and reading constantly. He asks the other homeless where the man has gone off to, and the homeless man is found to be named Tomida, who resides, or used to reside, in a tent with a plethora of umbrellas. Flashing back to Nakoshi's days as a businessman, it is shown that he took a taxi cab and eventually met Tomida face-to-face. It turns out that Tomida worked at a company that Nakoshi liquidated, unbeknownst to Tomida. Tomida begins chit-chatting with Nakoshi, and Nakoshi discovers Tomida's wife divorced him, and, too humiliated to work in Tokyo where he might be seen by former co-workers, took a job out in the country as a taxi-cab driver, and needs his son's support to make ends meet, much to Tomida's shame. Nakoshi searches Tomida's tent and is then overwrought with guilt as he finds old photos of his family in the book Tomida constantly looked at.
After observing a multitude of new homunculi in public, Ito finally gets back in contact with Nakoshi after his long absence. Ito hands over the rest of the money owed to Nakoshi, and explains that he is no longer interested in Nakoshi's ability anymore, and states homunculi to be nothing more than mere delusions. Ito is a bit shaken however, when Nakoshi says he can see a guppy within Ito's homunculus, and Ito had exactly the same fish within his bag. Nakoshi lies, however, and says that he saw Ito purchase it from an exotic fish store. Nakoshi, a bit angered at Ito's statement of homunculi merely being figments of his imagination, demands that Ito fix the hole left in his head. As the operation is getting ready to commence, Nakoshi notes that Ito's homunculus form resembles a tank of water in the shape of his (Ito's) father, with a single fish swimming throughout it. Before the operation can commence, Nakoshi makes several statements that rattle Ito, and Nakoshi then decides to, instead, have his right eye sewn shut. Nakoshi then begins trying to decipher the meaning behind Ito's homunculus. Nakoshi states that he "got involved" with the Yakuza and the clothing girl because he had similarities to both of them, and, theoretically, he should have some connection with Ito as well. After several unsuccessful attempts at unraveling the mystery, ranging from paternal problems to homosexuality, Nakoshi begins to lose hope, until he notices the fish inside the "body tank" of Ito has begun to resemble Ito, growing a face and legs.it:Homunculus (manga)