* Index's HeroicSafeMode in the first arc, what with the CreepyMonotone and the general "something's freaking wrong with her" atmosphere.
* Touma [[spoiler: getting his right hand cut off]], and then just [[LaughingMad laughing insanely while bleeding everywhere.]]
* Particularly [[spoiler: during the time when Vento attacks Academy City and Aleister sends Hound Dog to retrieve Last Order.]]
* Don't become [[spoiler: Etzali's]] enemy. He can attack your friends, hide their bodies, and then take their places without you noticing.
* Shizuri Mugino after she [[spoiler:CameBackWrong.]] She gains[[spoiler:GlowingEyesOfDoom]] and her already [[{{Yandere}} freakishly]] [[AxCrazy crazy]] personality makes matters even worse. She even threatens to [[spoiler:burn off Rikou's virginity]]!
* The Agnese Forces [[spoiler:sticking pens into their own ears and bursting their eardrums all to just stop the main effect of [[BrownNote Index's current spell]].]] The casual ease with which they did it really reinforces the fanatic feel of the forces and makes the danger far more real when not even '''basic survival instinct''' can stop them.
** What's worse is that Index's spell was pointing out contradictions in their ideology, effectively beating them over the head with their own hypocrisy. They're so brainwashed and crazy that they don't care how wrong they are. Case in point, the nuns who already experienced it instantly try to kill them again.
* When Sister Lucia uses her "carriage wheel shrapnel attack" on Touma. The shrapnel ''embeds into Touma's arm, then rips itself out!''
* What happened to [[TeleportersAndTransporters Musujime Awaki]] when she messed up her calculations and found part of her leg [[TeleFrag stuck in a wall]], removing the leg also removed the leg's skin and '''muscle'''.
* New Testament 2: [[spoiler: When the Radiosonde Castle was finally brought down, the message left on it was for Touma. This ordinarily wouldn't be anything new, but the tone it set indicated they blamed him for what they lost in WWIII and ItsPersonal. The message, written messily in red spray paint: ''Welcome home, hero.'']]It's worse if you consider that [[spoiler: [[ThereIsNoKillLikeOverkill they destroyed mountains and rivers to track him down by rearranging the planet's leylines and nearly caused an Ice Age that would destroy humanity]]. And they did it ''casually '' just to track him. God's Right Seat wasn't that bad compared to them.]]
* The TomatoInTheMirror scene where [[spoiler: ''Hyouka Kazakiri's head breaks open.'']]
* New Testament 3: [[spoiler: Cendrillon, using magic based on "Literature/{{Cinderella}}", can remotely mutilate the feet of anyone who has feet of a different size than hers. Worse, Accelerator explains that if she had used it on him, he wouldn't have been able to block it. The spell ignores distance and obstacles to affect the target instantly, so there are no vectors for him to redirect.]]
* The various forms of BodyHorror GREMLIN inflicts on [[YouHaveFailedMe failed]] or [[YouHaveOutlivedYourUsefulness outlived]] henchmen.
* What happened to Misaka WORST, [[spoiler: being cut open.]]
* Marian Slingeneyer's [[BodyHorror human modification magic]] and [[AndIMustScream how she]] [[CruelAndUnusualDeath uses it]].
* Don't piss off a RealityWarper or he'll suspend you in the air and instantly remove all of the skin from your body. Complete with three close-ups: an arm, the beating heart, and the staring "face". Much worse in the novels, where the character's innards in mentioned scene explode across the room after WITH BLOOD VESSELS AND ORGANS STILL INTACT AND CONNECTED WITH EACH OTHER. Despite this, the person happens to be still alive. And let's not get into any of the sequences that include the clone of said RealityWarper, (thankfully) edited out of the anime adaption.
** Exclusive to the light novels: Aureolus Izzard [[spoiler: Made a copy of himself that had his memories and thought it was him. It goes crazy when it figures out the truth, and has the power to turn anything it hits with its dart into molten gold, even people.]]
* Accelerator. Pretty much anything he does while in violent mode, including [[spoiler: brutally killing 10,000 teenage girls, chewing on at least one of those girls' fingers, executing a team sent after him in the most traumatizing and MindRape -y ways possible.]] And then you factor in his Powers which make him more or less invincible. Unless you are stronger than a nuke or happen to have an ability that trumps his and he can't adapt to (so far, only Touma), he is essentially unkillable.
** Perhaps his most gruesome kills were made during the Invasion by Vento of the Front, when [[spoiler:Hound Dog kidnapped Last Order]]. [[https://www.youtube.com/watch?v=criARmG7wx4 This happens when they try to pursue him.]]
** The scene is more gruesome in the light novel, [[spoiler:where he chews on a blob of flesh that he blew off of a fallen Hound Dog's jaw using his looted shotgun, looking far more deranged than any other illustration that he was featured in prior.]]
** What Accelerator [[spoiler: does to [[JerkAss Kakine Teitoku]] in the finale of the Battle Royale Arc counts, [[KickTheSonOfABitch though to be fair, he really did deserve it after what he did to Uiharu and Yomikawa]].]]
* New Testament 6: [[spoiler: Fraulein Kreutune has grown a monstrous mouth and is driven by instinct to try to eat Last Order's brains. Kakine Teitoku has come back, looking like a white zombie. He's also created an enormous army of copies of himself, as well as demonic rhinoceros beetles. [[FightingAShadow They are all him]].]]
* New Testament 7: Swarms of man-eating cockroaches that can also chew through metal, concrete, rubber, and plastic.
* New Testament 8: [[spoiler: Ollerus and Fiamma of the Right ambush Othinus and attempt to turn her into a fairy to make her weaker, only for the attempt to [[NiceJobBreakingItHero make her a perfect Magic God, no longer restricted by the 50/50 paradox]]. She apparently kills them both. She apparently makes Touma's companions disappear and gloats that everything that has happened has gone according to her grand design, then pulls Gungnir ''[[EyeScream out of her eye]]''! Touma desperately charges at her, only for her to declare, "These small fights are such a pain. I think I'll just end the world." Everything, save for Othinus and Kamijou Touma, is apparently annihilated, and the accompanying illustration is a completely black page.]]
* New Testament 9: Imagine yourself in Touma's shoes, [[spoiler:trapped in an endless cycle of alternate worlds. Having everyone hate you, even your own parents and teacher, then having someone take your identity, then getting eaten alive, buried alive, paralyzed in a hospital bed and left to rot, and trapped in a pod and launched into space all alone.]]