A Certain Magical Index/Tear Jerker

There some moments in this series that will just make you cry.

• Episode 6, when Index discovers from Touma's doctor that Touma's memories are destroyed but although Touma doesn't remember her, lies playing a joke to her to ease her.
  • Also a Crowning Moment of Heartwarming: "Touma... don't you remember? Index... Index... loved you, Touma..."
• This troper was reduced to tears watching Touma's You Shall Not Pass moment with Mikoto.
• Episode 17, Touma trying desperately to save his father from getting killed, only to get his ass handed to him. Then, Touma begging Motoharu not to sacrifice himself, before Motoharu explodes in a geyser of blood.
• Episode 20, Accelerator regretting he is unable to save anybody and redeem himself.
• Volume 14, Mikoto finally finding out about Touma's amnesia.
• In Volume 16, Itsuwa trying so hard to save a dying Touma after his battle with 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 fall into despair after being forced into a Sadistic Choice -- 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 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: Touma stops the Star of Bethlehem and crashes it into Gabriel to stop her (accidentally) bringing ruin to the world, but might be dead. If that's not enough, Mikoto had originally come to Russia for the express purpose of saving Touma, but he outright refused to be saved by her because he still needed to defeat Gabriel. Mikoto goes through the wreckage looking for him, but all she can find is the phone strap they got together a month before.
• New Testament Volume 4: Despite being able to prevent the deaths of many other people, Touma ultimately fails to save Kagun.
• New Testament Volume 6: After escaping the Windowless Building, Fraulein Kreutune runs across Last Order and Fremea and becomes friends with them. However, she becomes consumed by an urge to eat Last Order's brain, to gain the information needed to metamorphose. Thankfully, the urge is taken away when she's fed a realistic fake of the brain.
• New Testament Volume 9:
  • Touma is forced into a world where absolutely everyone, loathes him and wants him dead. He runs into both Seiri and Pierce, who both try to kill him and manage to badly injure him. Finally, he's fatally stabbed by Komoe-sensei, of all people. As he's dying, he hears an announcement regarding his parents, and fears that they've been persecuted for their relationship to him... only for them to denounce him as well.
  • After managing to withstand countless hells, Touma encounters something that absolutely breaks him - a world where everyone, except him, has been saved. By his standards, and the standards of most people, this would be a utopia worth preserving - meaning that he can't bring himself to fight any further. At Othinus' suggestion, he attempts suicide, only being prevented from doing so by the Will of the Misaka Network. In a rant to the Will, he admits that he doesn't want to die and wants to go back home, yet he doesn't want to destroy this perfect world.
• New Testament Volume 10: After a painful journey through a bitterly-cold landscape, Othinus refuses to be saved and uses the Fairy spell to kill herself, crumbling away in Touma's arms. Only a literal Deus Ex Machina stops her from actually dying.
• New Testament Volume 11:
  • Ayu's backstory. She used to be a normal girl who was friends with Touma, but she discovered that Academy City concentrates its resources to develop the powers of promising espers, while ignoring people like her. She tried to commit suicide, but at the same time was reluctant enough to call Touma for help. However, he was unable to do so due to pure chance - he bumped into Misaki and dropped his phone, preventing him from getting there on time. Ayu's suicide attempt failed, and she became involved with the dark side of Academy City. She became consumed with thoughts of revenge on Misaki for taking everything from her.
  • This volume reveals the past between Touma and Misaki... and also explains why Misaki normally avoids him. Due to brain damage, he hasn't just lost his memories of her, he can never form new memories of her.
• New Testament Volume 12:
  • Shinka pretends to be the #6 Level 5 and enters the Dianoid with one purpose - to find Frenda Seiveluin. But the reader is already aware that she's dead - and was killed in a gruesome fashion. When Shinka watches footage of the murder, he breaks down.
  • Touma and Shiage find a room in the Dianoid rented by Frenda, which she'd kept secret even from the rest of ITEM. It's filled with future birthday gifts for all of her countless friends - gifts that she's no longer around to send.
• New Testament Volume 14:
  • Patricia is infected with a strange parasite, forcing Leivinia to resort to dangerous magic in an attempt to save her. But since Patricia has no knowledge of magic, she doesn't have any idea what her older sister is doing, only knowing that Leivinia will die if she keeps going.
  • At the end, Nepthys sacrifices herself to heal Patricia, wanting to finally do something god-like.
• New Testament Volume 16: Touma encounters Misaki again when he's brought to Tokiwadai. While it's clear that it's painful for her to be around him, she still puts on a brave face.
• New Testament Volume 18: Aleister Crowley's backstory, which allows us to finally understand what made him the man he is today. He knew that his daughter would die from illness, and saw it as a consequence of the Magic Gods' actions. This led to his burning resolve to wipe them all out.