Anime/ Manga with Downer Endings (SPOILER ALERT)
A listing of anime/manga titles I've seen or read where the ending is downright depressing or sad for the main characters or sucks for everyone on the planet.
1. X

This implies with the crappy 1996 film adaptation of the series. In it, Kamui is the only surviving character in the end as all his loved ones and everyone among both the Dragons of Heaven and Dragons of Earth killed off with the final scene featuring Kamui decapitating best friend turned enemy, Fuma.

2. The Animatrix

This implies with the two-part "Second Renaissance" short that explores the events that led up to the robotic takeover from humanity. And of course, it sucks for humanity.

3. Grave of the Fireflies

The beginning of the movie from the get-go states that Seita and Setsuko will inevitably die by the end of the film. Both wind up dying from malnutrition with Seita a broken character with everyone in his family dying before him.

4. She, The Ultimate Weapon (TV)

The ending is different between the anime and manga, but both still wind up quite depressing in the end. Anime features Chise failing to stop an attempted enemy invasion as everyone on the planet winds up dying with Shuji the last remaining human who may or may not be hallucinating about Chise the little speck of light. The manga features Chise wiping out the remaining human population on Earth as she turns into a giant spaceship to take Shuji to a new planet where they can start a new life together.

5. Mahoromatic: Something More Beautiful

Depending on how you interpret the final scene of the anime, Suguru might be dying from wounds he sustained from a traitorous partner of his as the computer system for the Saints, Matthew, gives him a "final vision" of Mahoro.

6. Air

Misuzu's inevitable death coming from Kanna's curse. Could also be considered a bittersweet ending as Misuzu was able to repair her relationship with aunt Haruko before death and winded up breaking Kanna's curse thanks to Yukito's magic.

7. The End of Evangelion

Human Instrumentality Project, nuff said. XD

8. Texhnolyze

Everyone among the four factions fighting among one another, including main character Ichise, wind up dead from their bloody and intense gang war.

9. School Days

In the anime, Makoto is killed by Sekai for hooking back up with Kotonoha. Kotonoha winds up becoming mentally unstable as she severs the head of Makoto's corpse, kills Sekai by slicing her in the jugular plus cutting her stomach open and travels out to sea by boat while hugging Makoto's severed head. The manga features Kotonoha getting killed off by Sekai instead in the end so she can hook up with Makoto.

10. Berserk

The anime might have been open ended. But the point in the plot it chose to end was at the point where things started to become an absolute hell for Guts and Caska with the Band of the Hawk getting slaughtered by countless apostles, Griffith turning into Femto and Caska getting raped by Femto in front of a helpless Guts.

11. Jin-Roh: The Wolf Brigade

Kazuki Fuse winds up being forced by his superiors in the Wolf Brigade to kill his lover, Kei Amamiya.

12. Narutaru

The manga ends with the entire human population being wiped out by giant hands created by the Earth as a result of Shiina becoming mentally broken from the loss of all her loved ones and Mamiko going berserk with the power as a result. Both girls wind up the last living humans on Earth with both pregnant setting up an "Adam and Eve" scenario.

13. Wolf's Rain

Everyone on Earth winds up dead with Kiba failing to reach the gates of Paradise and his comrades being killed off by Darcia.

14. Gilgamesh

Everyone dies on Earth in an apocalyptic scenario triggered by the Countess of Werdenberg willingly allowing herself to merge with the creator of the Gilgamesh called Tear. Even with the newly created world desired by Tear, it is strongly hinted that the world would turn out no differently from the last one when Kiyoko's child winds up killing Tear because of her strong resemblance to the Countess from their merging.

15. Space Runaway Ideon

The most infamous example of a downer ending from anime and what earned Gundam director Yoshiyuki Tomino his nickname of "Kill Em All". Humanity and the Buff Clan wind up killing each other off in some messy ways and the ensuing battle results in both their home worlds being destroyed.

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