The destruction of the universe is frequently used in anime and manga as a major threat to motivate the heroes, but seldom is reality destroyed -- at least, for very long. However, sometimes the end of reality is unavoidable. While they are few and far between, here are five series where the entire universe does indeed get destroyed.
The Melancholy of Haruhi Suzumiya
The Haruhi light novels and anime center around the SOS Brigade, a school club assembled by Haruhi Suzumiya to help stave off her own boredom. While Kyon, the protagonist, is just a normal human being dragged into things, he finds his fellow clubmates consist of an alien, a time-traveler and an Esper. Haruhi, it turns out, is a God-like entity capable of obliterating and rewriting reality on a whim.
Three years ago, Haruhi destroyed the old universe, bringing all the characters into existence in the new one. Time travelers can't travel further back in time than that incident. Espers confront titanic entities spawned in this new world. More disturbing is that Haruhi wasn't even aware that she destroyed the universe. This is one of the few series to start in the aftermath of a universal apocalypse. While life continues, it continues in the place of a reality that disappeared three years prior and never came back.
JoJo's Bizarre Adventure
As is often the case, things get weird in JoJo's Bizarre Adventure. In the sixth arc of the manga, JoJo's Bizarre Adventure: Stone Ocean, the big bad Enrico Pucci plans on conjuring his Stand, Made in Heaven, to recreate the world in DIO's image. His Stand has the ability to accelerate time rapidly, pushing the Universe to the ends of time and triggering the Big Crunch, allowing him to recreate the world again.
Surprisingly, this cycle of death and rebirth cycles through twice in Stone Ocean, as the Universe is ultimately reset when Pucci is killed and his whole universe collapses again. This makes JoJo's Bizarre Adventure a rare example of a manga where the universe ends twice. The JoJo's Bizarre Adventure anime has yet to adapt this arc, though hopefully an adaptation will be announced sooner than later.
Puella Magi Madoka Magica
In Puella Magi Madoka Magica, the very universe itself is the real enemy. In order to stave off the heat-death of the Universe, an eldritch abomination known as Kyubey turns girls into magical girls after granting a single wish to combat witches. Inevitably, each magical girl turns into a witch. This cycle somehow, on a large enough scale, can stop the universe from dying.
When a young girl Madoka gets her chance to become a magical girl, she chooses to wish away the whole cycle of witches from existence, ascending to a state of Godhood. This wish literally rewrites the universe, destroying the old one by replacing it with a new one that functions under different rules.
Space Runaway Ideon
Yoshiyuki Tomino is famous for Mobile Suit Gundam, but Space Runaway Ideon is the show that earned him the nickname "Kill 'Em All Tomino." The series focuses on the titular Ideon, a giant robot assembled by three tanks found in deep space. Humanity uses the Ideon as a defense against the Buff Clan, an alien civilization. The Ideon demonstrates godlike power in battle. The television series ended on a bitter-sweet note, with the Ideon using its power to destroy both civilizations, under the caveat that they will be reborn, with a second chance to do things right next time.
The later film ending, Space Runaway Ideon: Be Invoked, took the story in a far bleaker direction. After the characters get brutally murdered in combat, the Ideon unleashes its full power by creating a shockwave that utterly obliterates all reality. While the series still features the souls of all the characters traveling to a new world for rebirth, it's uncertain if this world even exists in the same universe anymore. It's said this ending proved a huge influence on Hideaki Anno when ending Evangelion. By comparison, End of Evangelion is more optimistic.
Bokurano
Bokurano centers on a group of ordinary middle-schoolers transported to a foreign place in order to partake in a tournament. The kids pilot a giant mecha known as Zearth in order to fight other mecha, fighting until only one is left standing. While this sounds like a normal tournament anime, what makes it bleaker is the penalty for failure.
Each participant comes from an alternate universe. Should a participant lose, their respective universe is erased from existence. There are 32,768 different participants in the game, meaning that, if only one universe is left standing by the end, then 32,767 universes get destroyed by the end of the story. Unlike other shows with similar concepts like Dragon Ball Super, the destroyed timelines never return. In fact, it shows the horrifying obliteration of each world, with the stars radiating outward and swallowing up everything, leaving nothing but silence and darkness behind.
