Episode 12. Screaming psychic fetus monster fits the bill nicely.
Episode 23. Therestina. Think of Major's looks of madness, just that look of "I shall kill you, and it won't be a quick death," And amplify that to 11. And then add the idea that she's either doing this For Science!, or maybe just for power, but either way she has this unsettling look, a look that says "Don't fight, become a guinea pig." Brrr...
A huge amount of the "Sisters" story arc. The series depicts Mikoto's breakdown into despair a little too well.
Accelerator ripping off a Sister's leg and crushing her with a train car, then laughing about how tonight's "entertainment" is over.
Right when Mikoto thinks that it's all over, and is finally able to relax a bit after expending enormous effort, another Sister arrives and confirms that the experiment is on-going: Mikoto barely slowed it down.
Mikoto finally gives up and sees no way out of this situation except by sacrificing herself. The girl is ready to do something literally suicidal just to get this pain to end. Thankfully, Touma shows up to help.
Chapter 61. Where do we start?
Exterior is a giant brain formed from Misaki's. The purpose? Allowing anyone to use her powers. Anyone.
Gensei hijacking Exterior for his own use.
Even Gensei's line about Mikoto being "Aleister's favorite" is incredibly creepy in context. How long have they been planning to use her like this?
The chapter ends with a single, terrifying statement: "Now, let the experiment begin; Can Misaka-kun reach Level 6?", all while a demon-like Mikoto is just sitting there with an empty gaze Thanks for that, Gensei Kihara.
To make it worse, Mikoto is supposed to be able to No Sell those kinds of things. It's that powerful where it can easily overwhelm a Level 5, and mutate her entire appearance to boot.
Chapter 62: The possessed Misaka is apparently able to be controlled. And the ones doing it have no trouble nuking buildings as a testing method.
Seeing transformed Misaka stand there with an empty look just looks chilling.
Chapter 64. Just Chapter 64.
It's no longer a question of "Can Mikoto reach Level 6?", it's a matter of "Can they stop her from reaching Level 6?" To make matters worse, Touma can't stop the transformation even if he does touch her, he can only slow it down.
Mikoto becoming even less human-like. It's even mentioned by Gensei that when she's 53% of the way there, her personality won't be that of a human anymore.
Gensei is using Level Upper to give himself Multi-Skill.
The whole prospect of the experiment succeeding: Mikoto will die, and the entire city will go down with her.