* The DarkAndTroubledPast of the characters and how it affects their lives and gain eye powers because of those traumas.
* [[ManicPixieDreamGirl Ayano]]'s suicide and [[LoserProtagonist Shintaro]]'s reaction to it. While [[http://www.youtube.com/watch?v=oIQqGdfdR8Y&t=2s 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.
** Not to mention the fact that WordOfGod states that Toumei Answer was composed in-universe by Shintaro...and Ene deleted it...
** Oh, it's much worse than that. Ayano committed 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.
** Followed up immediately by Episode 11 of the anime, which expands on Ayano's suicide and implies that it was a SenselessSacrifice, since Takane and Haruka ended up dying anyway.
* 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.
** "Yuukei Yesterday" is a suitably adorable song about their relationship, right up until the very last chorus comes up and shows Takane running during sunset with tears in her eyes. [[LyricalDissonance the music doesn't quite match the lyrics here]], but it's clear that it's supposed to represent the RaceForYourLove moment mentioned above, [[ForegoneConclusion which only makes that particular scene more tragic]].
--> ''Hurry, before [[DeadlyEuphemism the sun sets]]...''
--> ''Oh God, please do something''
* Also, the medusae, suffering through FantasticRacism by the humans.
* 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.
* 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.
* 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 lyrics in the final chorus: The Shintaro that sacrificed himself accepts Ayano's death while the Shintaro that killed himself begs her not to leave him.
[[folder: Light Novel]]
* Kano's overall [[TraumaCongaLine backstory]] literally left the fandom in ruins. We knew it was sad... but not HEARTBREAKING.
** Kano is too self-conscious to actually laugh or smile around other people, so he uses his powers to fake it.
** Kano's powers are deactivated by pain. This is ''not'' an intrinsic part of his powers, but because Kano identifies himself so closely with pain.
** 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.
* Konoha sacrificing his life to save Shintaro: ''"Because we're friends..."''
* In the third novel, Shintaro reflects on how quickly he's adapting to life in the Mekakushi-dan. While it's sweet to see him connect with others, it leads Shintaro to realize how unhappy he really was as a NEET.
* This [[https://vignette.wikia.nocookie.net/kagerouproject/images/c/c5/Lost_Days_VII.png/revision/latest?cb=20150404100115 image]]. [[spoiler: Which takes place immediately after Haruka tells Shintaro that he only has a month left to live.]]
* In the seventh novel, Ene says that she stayed with Shintaro because she was afraid that he might kill himself if nobody did anything. Shintaro privately admits that she was probably right.
* 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"]].
* 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]].