Disclaimer: Naruto belongs to Masashi Kishimoto.
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When Uchiha Itachi was thirteen, he received a serious head wound as the result of misinformation on an ANBU mission. He was brought back unconscious to Konoha by one of the two subordinates who'd gone on the mission with him; the other's corpse had been dismembered and cremated a sufficient distance from the site.

The nurse who was changing his IV when he woke up was a woman Itachi had never seen before. She ran him through some basic tests to check his memory and reflexes, and thought he was as fine as could be expected in the situation. She left to turn in the notes and have a doctor sent to confirm them.

The doctor who came in ten minutes later was a man that Itachi had met before, and that was when everything ended.

They called it Capgras Syndrome: damage to a certain area of the brain left the patient in a situation where he could recognize faces, but not the attached emotional relationships. Auditory input worked fine, but not visual--the patient would recognize someone upon hearing their voice, and the recognition would last up to the moment that they were seen, at which point the certainty that they were an imposter would return.

For a ninja, especially one as severely trained and paranoid as an ANBU, this was a death sentence for their sanity.

It takes half the police force to track down Itachi after he attacks the doctor and flees the hospital; much of the reason they're able to catch him is because he's still wounded and he wasted nearly all his chakra keeping his eyes in the sharingan and trying to cancel genjutsus that don't exist.

When he's brought back to the hospital, he's kept in a drugged state while two doctors explain to Fugaku their suspicions based on the lack of drugs in his system, the location of the head wound, the repeated attempts at canceling, and the few words Itachi said to the police officers in the midst of trying to escape and kill them. The hypothesis is confirmed when Mikoto speaks to him from outside the door of his room, even using the Uchiha's passcode, until Itachi acknowledges her. When she steps into the room, however, his eyes harden and he immediately tries to attack again.

She leaves when he calls her an imposter, and three ANBU restrain him long enough for the doctor to sedate him again. His bleeding wrists are bandaged from where the metal of his chains have cut the skin.
-

A week passes.

There is some talk of scouting the other villages for a medicnin; Konoha's best tried, but each time they let Itachi off the sedatives it's discovered that it isn't enough. But eventually it is decided by both the Hokage and the head of the Uchiha clan that Itachi's body contains too many secrets to be entrusted to outsiders, regardless of the peace treaties.

They try therapy instead, hoping that if he's presented with enough evidence that it will finally override his instincts. Several ANBU members visit in the course of taking a post outside his room in case he manages to get out of the reinforced chains; Kakashi reminds Itachi how the boy was the one who gave him a hint on how to increase the power of the sharingan, and Itachi replies that it was a shame the real Kakashi still hadn't managed to be strong enough to keep from being tortured until he gave over information. Kakashi writes him off in his mind and leaves. Much of the same occurs with Shisui and the police officers.

When his father visits Itachi grills him over the most minute details of the clan and finally attacks the man with the sharingan; Fugaku responds in kind and for just a second, before Itachi's ANBU features settle over his face again, thinks he sees the beginning of a suspicion of the truth in Itachi's eyes.

He leaves the hospital room and gives orders that Shisui be kept away from now on.

After two weeks Itachi stops fighting and starts eating the food he's given, but he also stops speaking. The hospital needs his bed; Fugaku arranges with the Hokage for Itachi to return to the Uchiha compound. The next night, the boy is sedated to complete unconsciousness and moved to a windowless room in the main house, with a double barrier threaded inside the paper walls to keep him from getting out.

When he regains consciousness, Itachi thinks to himself that when he finally breaks free of this genjutsu, he is going to keep the person who cast it on him alive until he learns it himself.
-

For the next month, life is quiet and painful. He gauges time in the movements of the household, and the sound of Sasuke going to and coming back from school.

He never turns the sharingan off while he is conscious, which is less often as he drains his chakra reserves to exhaustion. His mother, discreetly armed, brings him meals unless she's on a mission, in which case a third cousin, someone from her family before marriage, does. His father questions him sometimes from outside the walls. Itachi never answers. He can hear Sasuke distantly once in a while; the child was ordered to keep away from the room, told only that his brother is injured and needs rest. After thirteen days pass and Itachi is still hidden away, Sasuke sometimes sneaks over in the middle of the night and talks to him. Itachi knows he can't be real, not in the swarm of imposters outside these walls, and tries to ignore the sense of home in his childish rambles. He always tells Sasuke to go back to bed after a few minutes.

After seventeen days he starts to wonder if Sasuke was kidnapped and is also being controlled by a genjutsu. It shouldn't be possible, not if he's still in one himself which he must be, but Itachi tried to find another explanation for Sasuke's reality and could think of none.

Whenever Shisui doesn't have a mission, he sits in the hallway outside Itachi's room and talks to him, cleaning his weapons or armor or repairing his clothes as he does. Itachi can see the shadow of his head and neck above the wood paneling of the wall, and can hear his hands move.

What Shisui talks about are meaningless things at first: family gossip, village gossip, other villages' gossip, politics and his girlfriend and all the minor cases in the station. Itachi's replies are noncommittal, and after twenty-two days Shisui attempts to restart the philosophical conversation they were having before the boy went on his mission. Itachi doesn't speak at all after that, and Shisui eventually gives up and leaves. Itachi strains to hear him go, and listens as Mikoto asks if he wants to stay for dinner. Shisui turns her down politely.

When he comes back the twenty-third day, Itachi leans against the part of the wall where Shisui is sitting opposite, stares up at the ceiling that he's memorized and begins to talk. He knows the genjutsu has broken him, and keeps all the clan and village secrets, but he tells Shisui everything else: that he knows the young man is an imposter no matter how real he sounds, that he wants to see his brother, that he is going to kill him once he's free of this genjutsu, and that he will go insane before he will tell them anything. At some point he begins talking not to Shisui but to the man creating his fake in Itachi's mind.

Shisui listens in silence, and finally sighs and stands.

"Come on, Itachi," the young man tells him, and Itachi can picture the shape of his shadow on the wall and doesn't turn his head to look at it. "We explained what happened to you. What Uchiha would allow the secrets of the sharingan to be revealed to some enemy? Do you really think it's more likely that we're all fakes and you're correct?"

Itachi doesn't answer, and Shisui leaves.

That night, listening to Sasuke brag about his work in class that day, Itachi decides that he has died in this genjutsu, and because that is impossible, decides to prove himself wrong.

On the twenty-fourth day, he carefully begins laying the foundations that he knows they want to hear. For the next few days he lets Shisui prod him into admitting the impossibility of the sharingan's techniques falling into others' hands, lets the young man remind him of how his father had used it in the hospital, speaks a fraction more politely to his mother when she brings his food, and finally acknowledges his father when the man begins speaking to him again. When Sasuke comes by at night, Itachi tells him that he's getting better and Sasuke needs to go back to bed--he's going to affect his performance in class by sacrificing sleep all the time.

After thirty-three days, his mother opens the door to the room and asks if Itachi wants to eat breakfast in the kitchen.
-

It was the easiest to remember that his mother isn't real, because of the near-daily reminder. His father was a little harder, but not too much, since the man rarely spoke to him between the first week and the last. Shisui was almost impossible, but he managed.

Itachi is disgusted with himself when he discovers that Sasuke is an imposter as well. He is supposed to be better than this.

He smiles at the fake Sasuke, who paused in the middle of taking off his shoes when Itachi stepped up to the entryway and immediately asked how he was, and tells him he still feels a little sick, but he's trying to get better. He is well aware that the fake Mikoto is listening from the other room.
-

Another month passes, and Itachi walks a fine line between a lie and a truth--he tells the fake doctors he is required to visit before being permitted back into any kind of duty that he still feels he is surrounded by imposters, but knows that no genjutsu could last this long. He is eventually restored to ANBU status, but required to work with others from now on. Itachi accepts the condition with an understanding nod. It is more difficult to remember that the others he works with are fakes when they wear their masks, but he reminds himself that anyone capable of imitating an ANBU in the first place would have be that talented.

He still practices canceling techniques, when he is alone.

His conversations with the fake Shisui are hesitant at first, the right level of awkward considering the last two months, but eventually they are nearly back to where they were, arguing philosophy and the true meaning of a shinobi and the fake Shisui reporting his words to the fake police. Very little changes, in the end.
-

When he kills Shisui, he doesn't know why his eyes burn afterward. This wasn't his friend.

By the next morning, however, Itachi accepts that he is insane. He has been in the genjutsu for so long that his mind has begun to accept falsehood for truth--but only to the point in which it aids him. When he later kills all the other Uchiha, he feels nothing. It helps that now they can no longer speak around corners or behind doors or from beneath masks, confusing him.

Since the Amaterasu form of the mangekyou has specific requirements, he leaves Sasuke alive as well, in case he is so insane that his mind will acknowledge the child as a blood relation.

And even if he isn't, he'll still win--once the spy returns to where he came from, the news of what Itachi did will get back to the real Konoha and the real Uchiha, and they'll come for him.
-

Once he gets outside the village walls, Itachi can't understand why no matter how far he goes the landscape won't stop being familiar. He travels as far as possible the first night, tries to cancel the genjutsu again--more from habit now than belief that it's possible--and finally conceals himself in the roots of a tree and falls dirty and exhausted into sleep.

Everything is the same in the morning. He is still in Fire country.

Itachi avoids towns and people after that, afraid of the unknown in a way he can't remember feeling even as a child, unwilling to attract as much attention as he would by killing so many. The only time he enters towns is when he runs low on clothes or rations, and then he only goes at night and breaks into whatever store is necessary.

He travels enough to keep the hunternins, real or fake, away. Mostly he trains, and acquaints himself with the mangekyou sharingan. His birthday, and then the rest of the year, passes.
-

Kisame is the first real person he sees in a long time.
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After they've failed to kill each other, he wraps his wounds and listens to Kisame explain about the Akatsuki. When the man offers him the ring, he accepts. He has nothing better to do; he is still waiting.

Kisame agrees that he's insane, saying it takes a certain kind of person to kill every single relative they have, but doesn't seem bothered by it. Itachi understands why when he eventually meets the rest of Akatsuki. He never corrects the other man's misunderstanding--it would be humiliating to admit how long he succumbed to that genjutsu.
-

It takes him three years to walk back into Konoha, and there he is forced to consider, for the first time, than he was told the truth. Itachi knows many genjutsus, and none of them can compel a person to believe that a full four years have passed. Even the mangekyou is only capable of a maximum of three days.

Kisame never comments on how long they take fulfilling their assignment regarding the bijuu. Itachi appreciates that.

The assignment fails, and like vinegar in the wound he learns that the bijuu wasn't even in the damn village; but then in the hotel corridor he hears Sasuke's voice behind him and Itachi thinks that finally, after all this time, the news got back. His waiting is over.

But when he turns around, all he finds is the imposter.