* [[ManicPixieDreamGirl Ayano]]'s suicide and [[LoserProtagonist Shintaro]]'s reaction to it. While [[http://www.youtube.com/watch?v=oIQqGdfdR8Y Toumei Answer]] was pretty heartbreaking, it is handled very quickly and matter of factly. But then you realize in [[http://www.youtube.com/watch?v=9uvosToqE-8 Ayano's Theory of Happiness]] that the poor girl had bonded with most of the cast of the series and they loved her so very much.
** Oh, it's much worse than that. Ayano commited suicide because she wanted to gain an eye ability in order to protect Kido, Kano and Seto from her father, who had reached the DespairEventHorizon and killed Haruka and Takane in an attempt to bring Ayano's mother back to life.
* Not to mention just how upsetting [[https://www.youtube.com/watch?v=v9wrDGfYCWA&list=FLMi7MeSPNCHjVpCCs4RrN4g&index=24 Lost Time Memory]] was. In both routes, Shintaro struggles to find himself and move on from her death by keeping the memories of her with him forever. In one timeline, he succeeds. In the other... [[DrivenToSuicide not so much.]]
** Made even worse when you see Jin's comment in the description. 'I still loved you, today too.…'
* The GroundhogDayLoop Hibiya and Hiyori are forced to live in [[http://www.youtube.com/watch?v=d1lO387FrUg Heat-Haze Days]]. Poor Hibiya is forced to watch Hiyori die in increasingly horrible ways, no matter how much he tries to prevent it. In order to break the loop once and for all, he goes back to the first death and sacrifices himself so the girl could live. And it was a SenselessSacrifice, as Hiyori sacrifices herself so Hibiya can live and break the loop once and for all.
* Anything involving Konoha/Haruka Kokonose. An IllBoy who wished to have a strong body. It is granted...but he goes through UnwillingRoboticisation and IdentityAmnesia so this could happen. BeCarefulWhatYouWishFor, indeed.
* Also poor Ene/Takane Enomoto, his closest friend and classmate. She had a really big crush on Haruka, but due to her Tsundere personality (that was caused by her disorder) she never really got to express those feelings in other ways than pouts and fists. Then, during a test, Haruka got his final attack and died. This went unnoticed for Takane, who had turned her headphones on while facing the other way, for 20 minutes. When Kenjirou then lied to the heartbroken Takane, telling her that he survived, she finally, with the help of Ayano, managed to get her resolve up and tell Haruka her true feelings. Only that it didn't happen. Because she was KILLED before she reached the hospital. Two years later, in the form of the computer program Ene, Takane met the brought-back-to-life-through-robotication Haruka again, but it turns out he had gotten an IdentityAmnesia and didn't remember her.
* Also, the medusae, suffering through FantasticRacism by the humans.
* The DarkAndTroubledPast of the characters and how it affects their lives and gain eye powers because of those traumas.
* Ene's reaction to Shintaro deleting her in [[http://www.youtube.com/watch?v=hN_UJHwDFk0 Jinzou Enemy]]. Despite trying to become a ManicPixieDreamGirl for his sake and in an attempt for trying to fullfill the role Ayano couldn't do, he still sees Ene as nothing but a shallow program for talking to and deletes her.
* All the hell poor Marry has gone through in [[http://www.youtube.com/watch?v=Ui4TXA9oFmg Outer Science]].
** And Azami has it just as bad, watching everything go straight to hell just because she wanted to be with her family.
* Kano's overall [[TraumaCongaLine backstory]] literally left the fandom in ruins. We knew it was sad... but not HEARTBREAKING.
** It doesn't help that he's not even able to ''laugh'' on his own. He has to use his powers just to ''giggle''.
** Well he ''can'' laugh on his own, he's just too self conscious of his real laugh/smile to actually do so.
** Kano's breakdown in the last chapter is pretty heartbreaking, especially since, until this point, we've basically only seen him smile and joke around.
* The anime's [[https://www.youtube.com/watch?v=DUMnmBozJ7M ending theme]], coupled with the visuals, can be quite heartbreaking.
** The [[https://www.youtube.com/watch?v=2sPDPr3S7Zg PV]] for the full version isn't much better.
* Episode 10 of the anime, which might as well be titled [[Anime/PuellaMagiMadokaMagica "being medusa is suffering"]].
* Followed up immediately by Episode 11, which expands on [[spoiler:Ayano's suicide]] and implies that it was a SenselessSacrifice, since [[spoiler:Takane and Haruka ended up dying anyway]].
* According to [[http://furiwokaaan.tumblr.com/post/90733082048/some-few-stuffs-from-the-spoon-magazine-ah-ahaha an interview]] done after the last episode of the anime, [[spoiler: Konoha was KilledOffForReal, and Shintaro misses him]].