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.
- 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.
- Volume 22 light novel: Touma stops the Star of Bethlehem and crashes it into an Angel that was (accidentally) bringing ruin to the world, but might be 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 Maika was murdered. Fortunately, it turned out to be a false alarm, but the two were pretty much broken before they learned that.