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All but two or three of the fish were dead. The full tank of fish in Rumi's replica of Mima's apartment is what helped Mima realize she wasn't actually in her own room.
The scenes where Mima chases a vision of herself in the pink girly ballerina outfit.
The scenes where she is being photographed naked by the borderline-rapist pornographer Murano.
The scene where she supposedly stabs Murano in the eye and then his crotch before chasing the man throughout his house and then repeatedly stabbing him to death with an vicious look on her face as he screams in terrible agony.
How Mima starts to hallucinate and sees Me-Mania's horribly ugly face everywhere.
Or was he 'really' stalking her?
Also with the fact that we'll never really know if it was stalking or her hallucinating.
If they were hallucinations this opens up more on whether or not it was really Mima at the end and whether or not she'll go through a similar thing later.
The scene where Me-Mania accosts Mima and attempts to rape her with a crazed grin on his face.
"I guess I went to Harajuku today..." Ho-ly loss of identity, Batman!
In a major twist, the true villain in the movie turns out to be Mima's middle-aged female manager Rumi, who was a former pop idol who didn't last and now thinks she's the real Mima. The climax of the film where Rumi chases Mima in the illusory form of Mima's giggling, pop-idol alter-ego while trying to kill her is genuinely disturbing.
Of course, that's if you think that Rumi isn't in fact the real Mima. By that point in the movie, it's no longer possible to be sure.
Just to review, Rumi at one point chases Mima down a street in front of a series of storefront windows. In the foreground chasing Mima is Rumi in the idealized form of Mima's pop-star alter ego, laughing and skipping down the street without a care in the world. In the background, every time Rumi passes in front of a window, you see her real form reflected: an older woman clutching an ice-pick/umbrella, gasping and snarling while in a dead sprint.
The worst part is that this appears to be a shared hallucination; Rumi thinks she's Super-Innocent-Magical-Avenging-Angel Mima, and Mima also thinks Rumi is Super-Innocent-Magical-Avenging-Angel Mima. For once, the viewer is shown the truth, while the characters can't see it — and you of course can't do a God damn thing about it.
The guy in the parking lot who heard fragments of one of Mima's songs, then discovered a radio on the elevator's floor, when the doors opened. And a few minutes later the doors opened again to reveal him dead, covered in his own blood, and his eyes gouged out. He was the man who wrote Mima into a rape scene; "justified" would be absolutely the wrong word to use here, but there's a fairly obvious reason why Rumi (or was it Me-Mania?) killed him.
In the anime's denouement, Rumi is permanently delusional and institutionalized. It's quite unsettling. And her hair now looks just like Mima's.
Mima holds a tea cup in her hands in one scene and squeezes so hard that she breaks it. She's out of touch with reality at this point and while Rumi reacts with horror Mima simply looks at the blood with a blank look and says "This blood... Rumi is it real?"
The depiction of Mima losing touch with reality.
Mima's slow descent into madness is done so well that the audience has great difficulty in figuring out what's going on. Towards the end of the film, the amount of jumpcuts go up and Mima starts losing time - an unfortunate real life symptom of DID - and the repeats of her waking up in her apartment makes it feel like either days or weeks could have passed.
Mima: It's been a while, Rumi.
Rumi: What are you talking about, Mima? I was just here yesterday.