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.]]
* New Testament Volume 11:
** The backstory of [[spoiler: Mitsuari Ayu. She was a normal girl who was friends with Touma. She discovered Academy City had decided to focus money and effort into levelling up Misaki instead of her because they have the same power. She tried to commit suicide, making one last attempt to get Touma's help, who couldn't answer because he had lost his phone when he crashed into Misaki. Ayu not only discovered Misaki was the reason she had not been saved, she saw Misaki "take her place" after being saved by Touma. She's consumed by envy and a desire of revenge towards Misaki and is fully aware of how twisted she has become, which is the real reason why she wears the Five Over OS, she doesn't want Touma to see what she had become.]]
** Even if Touma wasn't ObliviousToLove, it's ''impossible'' for him and Misaki to have a relationship. [[spoiler:Due to brain damage he got a year before the series started, he cannot retain memories of her for more than a few minutes. The day after he rescues her from Mitsuari, he remembers fighting the attacker, but not her. She kisses him on the forehead and sadly remarks, "[[AmnesiacLover Ah ha ha. Don't worry. You'll forget all about it soon enough.]]"]]
* New Testament Volume 12
** Touma did not leave the events of New Testament Volume 09 unscathed. It shows in the worst way possible for him when [[spoiler:he first meets the elderly looking man in a tailcoat who claims to be a Magic God. In stark contrast to a couple of parts earlier where he casually waves off someone who claimed to be the 6th Level 5, Touma becomes incredibly cautious. However, when the Magic God started his assault by sending an innumerable number of spikes at him through large holes created in the unaware bystanders, his memories of the events of New Testament Volume 09 resurface and cause him to, after a long train of thought in which he compares fighting a Magic God to traversing a desert while clinging to the futile hope for an oasis, tell himself that there is no chance for victory. When the assault spontaneously stops, Touma drops any optimism and fears that a new phase may have been created and that he may have to go through the endless labyrinth of phases again. After the Magic God leaves, Touma is found by Index and Othinus. At this point he breaks down screaming and tearfully asks Othinus whether he is still in the same phase Othinus returned them to at the end of New Testament Volume 09.]]
** Touma and Shiage enter Frenda's hideout in the Dianoid:[[spoiler:It doesn't contain a new type of bomb. Frenda was the person in ITEM with most connections, claiming to know thousands of people both inside and outside AC's darkness. She had used the hideout to store all the birthday gifts she had meticulously researched and prepared for her numerous friends, including Mugino. The hideout was the only place where she could be herself and not a contracted killer or Fremea's older sister.]]