'''''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 Franchise/{{the Matrix}}, 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 had a compulsion about masturbating at work. When he turned in his resignation letter, he did it on his desk as well.
* 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. [[spoiler:Trepanning Nanako helped her and Nakoshi to see each other's homunculi, but there may have been dire consequences.]]
* AttractiveBentGender: [[spoiler:Itoh]] is constantly called "pretty" when he's dressed as a woman.
* TheBlank: Nanako's homunculus in its true form is a completely blank face, with comparisons to the [[https://en.wikipedia.org/wiki/Noppera-bo noppera-bo]]. [[spoiler:Eventually, it morphs into a bowl-like shape in which Nakoshi's original face is mirrored.]]
* BlobMonster: Yukari's homunculus is that she turns into sand which breaks and reforms in disturbing ways to move and has a nasty habit of taking unsettling forms and seeming to infect what it touches.
* TheCasanova: Nakoshi [[spoiler:after getting plastic surgery]], 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 homunculi 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.
* EvilDetectingDog: A suitably weird twist. Yukari's family's dog barks furiously when [[spoiler:the homunculi of Yukari and her mother manifest as a symptom of their tension]].
* 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 realizing Nanako's role in his life and freeing himself from the Homunculi. [[spoiler:[[DownerEnding The exact opposite happens]]: he throws Nanako aside (after ''trepanning her''), stays prisoner of this world and totally loses it, [[GoneHorriblyWrong even trepanning himself two more times]]. Additionally, given Nanako's final scenes and the people Nakoshi is running toward in his final scenes being dressed like cops, it's possible that she died from blood loss.]] [[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: The homeless in the park call Nakoshi "Car Guy" since he lives in his car.
* 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 seems to be one at first, but turns out to be pretty mentally sound [[spoiler:aside from his repressed gender issues]] and comes to regret what he's done.
* 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 [[spoiler:especially since the final shift is Yukari throwing her sexuality in her mother's face]]. Also subverted in the semi-rape in so far as that Yukari says she felt nothing.
* OfCourseImNotAVirgin: Itoh.
* OurHomunculiAreDifferent: Averted, they really ''are'' different.
* SelfHarm: Yukari habitually cuts the back of her left shin to cope with her mother's controlling, prying nature. [[spoiler:When her mother finds her and Nakoshi having sex in his car, she slams her foot against the window, essentially slapping her mother in the face with the bleeding wound.]]
* 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]].
* {{Transgender}}: [[spoiler:Itoh]], who eventually transitions.
* 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, [[spoiler:and that she may have died or at least suffered brain damage from the trepanation, judging by the blood seeping through her bandages and the police at the very end]], [[YouDoNotWantToKnow maybe it's better we don't]].
* WhichRestroomDilemma: [[spoiler:Itoh is shown deliberating over this when he excuses himself while crossdressing.]]
* WholesomeCrossdresser: [[spoiler:Itoh is made to crossdress by Nakoshi as part of his working through his homunculus, and ends up doing it on his own. Later on, it's revealed that he crossdressed as a child.]]
* {{Yakuza}}: They show up prominently twice. The first is a boss who Nakoshi sees as a blocky mecha [[spoiler:which is hiding himself as a young boy, a manifestation of his grief over a childhood accident where he maimed a friend]]. The second is one of Nanako's sugar daddies, who confronts her and Nakoshi over money Nanako stole [[spoiler:but leaves them be when Nakoshi helps him express his repressed grief over putting out one of his sister's eyes as a child]].
* {{Yubitsume}}: The Yakuza boss Nakoshi encounters with the mecha homunculus has taken ''many'' of his subordinates' pinkies. [[spoiler:This drive is a side effect of his repressed grief over cutting off his friend's pinky with a sickle as a child, and he finally exorcises it by performing ''yubitsume'' on himself.]]