'''''Homunculus''''' is a {{seinen}} manga, by Hideo Yamamoto, who also authored the manga which would become a cheerful little film called ''Manga/IchiTheKiller.''

So imagine that, like in Film/TheMatrix, you have a subconscious self image. It represents your deepest desires and fears. And no one can see it but you. You, and a homeless man named Susumu Nakoshi, who agreed to let [[MadScientist medical student]] Manabu Itoh drill a hole in his skull for a total of 700,000 yen. Itoh is interested in studying human minds, ESP, ghosts and the occult. And he thinks that he can potentially unleash the hidden psychic potential of Nakoshi's brain.

Nothing seems to be happening, until a few nights after the operation, Nakoshi briefly closes his right eye, and starts seeing nightmare-shapes and monsters everywhere with his left.

And then things get ''weird.''

Not to be confused with [[MobileSuitHuman the little people who live in your brain]], or with [[OurHomunculiAreDifferent other uses of the word]].

!!This manga provides examples of:

* AccentAdaptation: The scanlators translated Nakoshi's backwater [[TohokuRegionalAccent Tohoku accent]] as something akin to [[WesternAnimation/TheSimpsons Cletus the Slack-Jawed Yokel's]] bumpkin accent.
* ADateWithRosiePalms: Nakoshi.
* AllPsychologyIsFreudian: Although there is not as much sexual imagery (ignoring all the outright sex) as usually is associated with Freud, all the focus on repression and subconsciousness and the unconscious is enough to make any psychology student cry.
* AntiHero: Nakoshi can be seen as a deconstruction of the SamaritanSyndrome-inflicted hero - he goes around helping various people with their issues [[spoiler: so he can better understand himself and face his own.]] Not to mention that his method of "helping" is not always well thought-out or clear. When you try to save a girl [[spoiler: by raping her]], you know you're not quiiiite balanced in the head.
* AttractiveBentGender: [[spoiler: Itoh]] is constantly called "pretty" when he's dressed as a woman.
* TheCasanova: Nakoshi, before he decided to throw it all away because none of the women could make him feel anything.
* DysfunctionJunction: Justified, in that Nakoshi only associates with people whose homunculus he can see, meaning [[spoiler: he can only see the homunculi of people who have the same issues he does.]]
* EasySexChange: Averted by [[spoiler: Itoh, who takes a year to fully]] transition.
* FanDisservice: There's like two volumes straight of various characters masturbating and having sex. It's ''not'' played up to be hot.
** The sex scene in the final volume. [[spoiler: [[ScrewYourself Screw you, indeed.]]]]
* ForScience: Itoh's justification for doing the experiments.
* GainaxEnding: That's to be expected in such a MindScrew series. But this is made even more unsettling by the fact that for a moment it ''seems'' like we're heading towards a HappyEnding with Nakoshi freeing himself from the Homunculi… [[spoiler:the exact opposite happens: he throws Nanako aside (after ''trepanating her''), stays prisoner of this world and totally loses it, [[GoneHorriblyWrong even digging two additional holes in his skull.]]]] [[MyGodWhatHaveIDone Itoh himself is utterly horrified by how his experience turned]].
* {{Gonk}}: [[spoiler:Nakoshi and Nanako in their youth.]] And that's pretty much the cause of everything happening in the series if you think about it.
* HaveIMentionedIAmHeterosexualToday: Nakoshi and Itoh.
* InSeriesNickname: "Car guy" for Nakoshi.
* LovesMeNot: A variant - Itoh plucks petals off a flower, with the options [[spoiler: "man"]] and [[spoiler:"woman"]].
* LuminescentBlush: Adorably, Itoh frequently does this later in the series, starting from when he's forced to crossdress.
* MindRape: Nakoshi accuses Yukari of this.
* MadScientist: Itoh. Though he turns out not being that mad and even regretting the whole thing at the end.
* MindScrew: For both the reader and Nakoshi.
* MirrorMonologue: Nakoshi looks in the water and says that isn't his face - apt enough, considering [[spoiler: he had plastic surgery.]]
* MorallyAmbiguousDoctorate: Itoh again.
* NotIfTheyEnjoyedItRationalization: An extremely weird example. The sex scene in the car between Nakoshi and the schoolgirl Yukari goes from semi-rape to consensual to violent rape and back to consensual again. It's intended to be unsettling. Also subverted in the semi-rape in so far as that Yukari says she felt nothing.
* OfCourseImNotAVirgin: Itoh.
* OurHomunculiAreDifferent: Averted, they really ''are'' different.
* SparklingStreamOfTears: Itoh, [[spoiler:at the very end]].
* TomatoInTheMirror: When Nakoshi realizes that the homunculi he sees are [[spoiler: manifestations of his own inner distortions, which he projects on other people around him.]]
* {{Transsexual}}: [[spoiler: Eventually, Itoh]].
* TheUnreveal: Nakoshi finally finds [[spoiler:a photo of his pre-surgery face]] after quite some buildup and vague glimpses. It's variously covered up by the panel angles, a leaf, and even a dialogue bubble. The same treatment is given when Itoh later gets a look. [[spoiler:It is eventually revealed in the final volume.]]
* WellDoneSonGuy: [[spoiler: Itoh's entire motivation stems from a need to be acknowledged]] by his father.
* WhatHappenedToTheMouse: Nakoshi writes a kind word in the hotel room for Nanako saying he will be right back. He won't. In the epilogue he just says that Nanako was useless to him in the end and we never know what she became. And considering what he did to her, [[YouDoNotWantToKnow maybe it's better we don't…]]
** Given that the last panels of Nanako showed [[spoiler:blood seeping through her bandages, it's possible that she died or suffered brain trauma as a result of the trepanation, which would explain the appearance of the police and the series' abrupt dive into a DownerEnding]].
* WhichRestroomDilemma: [[spoiler:Itoh is shown deliberating over this when he excuses himself while crossdressing.]]
* WholesomeCrossdresser: [[spoiler:Itoh]].
* {{Yakuza}}
* {{Yubitsume}}