There some moments in this series that will just make you cry.
* Episode 6, when Index discovers from Touma's doctor that [[spoiler:Touma's memories are destroyed but although Touma doesn't remember her, lies playing a joke to her to ease her.]]
** Also a CrowningMomentOfHeartwarming: "Touma... don't you remember? Index... Index... loved you, Touma..."
* Touma's YouShallNotPass moment with Mikoto.
* Episode 17, Touma trying desperately to save his father from getting killed, only to get his ass handed to him. [[spoiler: Then, Touma begging Motoharu not to sacrifice himself, before Motoharu explodes in a geyser of blood.]]
* Episode 20, [[spoiler:Accelerator regretting he is unable to save anybody and redeem himself.]]
* Volume 14, [[spoiler: Mikoto finally finding out about Touma's amnesia.]]
* In Volume 16, [[spoiler:Itsuwa trying so hard to save a dying Touma after his battle with [[MadeOfIron Acqua of the Back]]. You can't help but feel her pain as his Imagine Breaker keeps involuntarily negating her healing spells.]]
* Volume 20 has the scenes with Accelerator, Last Order and Misaka WORST. Seeing Accelerator [[spoiler:[[DespairEventHorizon fall into despair]] after being forced into a SadisticChoice -- letting Last Order die in the hands of Misaka WORST or hurting another clone after promising to himself that he'll never do so again --]] is absolutely heartbreaking.
** Even earlier in the volume we get the scenes in the train, with [[http://www.baka-tsuki.org/project/index.php?title=File:Index_v20_037.jpg Last Order exhausted, barely able to speak and move, and Accelerator breaking inside because there's nothing he can do to ease her pain.]] His despair and anger about the unfairness of the situation is just heart rending.
* Volume 22 light novel: [[spoiler: Touma stops the Star of Bethlehem and crashes it into an Angel that was (accidentally) bringing ruin to the world, but might be [[OurHeroIsDead dead]]. If that is not enough Mikoto, who had originally come to Russia for the express purpose of saving Touma, goes through the wreckage looking for him after he outright refused to be saved by her because he still needed to defeat the Angel. All she can find is a phone strap they got together when she dragged him off on a punishment game "date" a month before.]]
* New Testament Volume 7:
** Touma and Motoharu hear a report that [[spoiler: Maika was murdered. Fortunately, it turned out to be a false alarm, but the two were pretty much broken before they learned that.]]
** Shiage comes up with a plan to [[spoiler: defeat Rensa]], but because Umidori wasn't able to trust him, it fails. Umidori bursts into tears when she realizes her mistake.
* New Testament Volume 9:
** World Alpha: Touma finds himself [[spoiler:in a world where he is Public Enemy #1. Everybody hates him and tries to kill him, blaming him for some unrevealed incident. He figures that his parents will be targeted as well and tries to find and rescue them... only to learn they want to kill him too. Then he gets stabbed in the back by ''Komoe-sensei''.]]
** World Omega:
*** Touma sees Index running in his direction and happily tries to greet her, only for her to run past him, as she doesn't remember him.
*** Touma's incredibly long rant where [[spoiler:he admits that Othinus is better than him in every way. Then he admits that he should be grateful that she created a world where everybody is alive and perfectly happy, but he isn't. He had never cared about being thanked or rewarded for his good deeds before, but he still '''hates''' her for making a world that doesn't need him; for making his life meaningless.]]