This is how AKIRA started... and ended (the movie at least).
Same with the manga (although the ending was under very different circumstances)... except that the manga has yet another Apocalypse about halfway through. All three have the same cause though (namely Akira).
It wasn't permanent, but late in Fullmetal AlchemistFather succeeded in turning the souls of everyone in Amestris into a giant Philosopher's Stone (Including shots of Dying Winry, Gracia, and Elicia, among many others), turned himself into a giant Living Shadow covered in eyes, ripped open the door to Truth, ate it, then turned into a younger version of Hohenheim.
Bokurano shows an Earth being consumed by an exploding sun, followed by every star in its universe blinking out of existence.
The final chapter of Elfen Lied has 10 or so pages dedicated to Lucy initiating The End of the World as We Know It while simultaneously repairing Kouta's gunshot wound. While singing. For comparison, 2 or so chapters are the destruction of the research facility, ending with it being annihilated from below. Why so short? Because that's how long it lasted.
Go Nagai's Violence Jack, after the introduction of its title character, spends the first chapter of the manga destroying Japan via massive earthquake and mass volcanic eruption before introducing us to the Crapsack World that the Kanto region has become.
In the final episode of Puella Magi Madoka Magica, Madoka's wish causes one of these in the process of rewriting the universe multiple times - with Homura watching the whole thing.
Dragon Ball Z's Frieza Saga had Frieza blowing up Namek, only for it to have a 5 minute delay (and a much longer one episode-wise). This is the only time that the destruction of a planet is not instantaneous in the series.
Heartcatch Precure, a usually happy-go-lucky magical girl series, has one. When the true Big Bad, Dune, arrives, he promptly curbstomps the heroines, kidnaps the lead's grandmother, regains his full power and turns Earth into a massive desert, the only survivors being the main heroines and the people whom they purified from being monsters.
V for Vendettaends with the exact event the plot's been building towards: The destruction of British Parliament. It might not even count as a Class-Zero, but dang was it well done.
The 2009 Star Trek film had the mightily impressive destruction of Vulcan.
Not before (well... actually, yes, before...) the destruction of Romulus in a super nova, which sparked off the whole chain of events.
Surrogates ends in a way with this, all the surrogates just shut down.
Subverted in The Hitchhikers Guide To The Galaxy. the Vogon constructor fleet has surrounded the Earth and are about to demolish it. You expect a spectacular explosion, but the Earth just disappears in a pathetically small puff of smoke.
Often this section is preceded by the words In a World [Earth explodes] but sometimes not.
Played straight in the TV miniseries, where Earth heats up to a brilliant red before detonating.
The original Nihon Chinbotsu(1973) featured an extensive sequence of Tokyo being swallowed up in the disaster done by Teruyoshi Nakano, who is nicknamed "Japan's Michael Bay" for his love of Stuff Blowing Up.
The 2006 remake didn't lack in the catastrophe department either, though it saved Tokyo (for last).
Lars Von Trier's Melancholia does it twice. At the start of the movie, the titular planet engulfs Earth while classical music plays. The movie also ends this way, but now we see the collision on a human scale from the Earths' surface.
Enders Game showcases precisely what Dr. Device did to the bugger homeworld.
Mark Geston's novel Lords of the Starship is about a vast rocketship that takes well over a century to complete, at which point two immense armies fight for control of it. Then the ship uses its rocket exhausts to incinerate the armies, and then reverses thrust to incinerate itself. Then the shadowy enemy that designed the ship in the first place sends a couple of city-sized fireballs to finish the job.
The great freezing at the end of Kurt Vonnegut's Cats Cradle, which sounded like "the great door of heaven being closed softly" and, within moments, caused the sky to fill with tornadoes.
At the end of Greg Bear's The Forge of God, the Earth's destruction is described in loving, agonizing detail.
Same for the asteroid colliding with Earth and breaking it into pieces in Remnants, near the end of the first book.
Though the actual Shattering is not described, the vivid imagery of huge fragments of landscape tumbling through the Void in The Shattered World makes it clear that the titular world's breaking must have been an Apocalypse Wow. The collision between two fragments in the sequel, The Burning Realm, gives an ominous preview of the surviving fragments' impending doom.
This happens in the 1933 classic When Worlds Collide, in the kind of spectacular fashion that you'd probably have guessed from the title. The 1951 film adaptation did the best it could with this, but the upcoming remake certainly should provide more of the disaster porn as described in the book, to say the least.
Arthur C. Clarke's novel The Songs of Distant Earth had its doomed planetbound inhabitants set up cameras to record images of the end of the Earth for the posterity of those stargoing vessels which just managed to escape its final destruction. Michael Oldfield's album The Songs of Distant Earth which is meant as an accompaniment to that novel has a music track that chronicles the Earth's destruction.
Clarke's early story (in fact, the first story he sold) "Rescue Party" also had the people of Earth set up cameras to beam images of Earth's end to the huge escape fleet in which they evacuated. It was following the line of those transmissions that led the alien rescue ship to the fleet.
The last remaining normal human broadcasts this at the end of Childhood's End.
The end of Narnia is described in detail at the end of The Last Battle — which, by no coincidence, heavily draws upon the Biblical Apocalypse.
The Ciaphas Cain novel Caves of Ice ends with the detonation of a gigaton range Fuel Air Explosive. It completely obliterates the sole settlement on the planet, and the shockwaves are felt by ships in low orbit.
The demolition of Vavatch Orbital in Consider Phlebas is so spectacularly donenote A Culture starship slices the ring in several places, and the Orbital's own spin makes it fly apart. Then they bombard the chunks with antimatter until they're smashed to atoms. Don't Fuck with the Culture., it almost qualifies as performance art.
In Lucifer's Hammer, Niven and Pournelle detail the end of the world with beautiful descriptions. The meteor leaves behind a fiery rainbow trail that blinds anyone who looks at it. The resulting multiple-impacts cause earthquakes and giant tsunamis all arond the earth, flooding entire mountain ranges.
And when they finally got around to finishing Footfall (Word Of God is the publisher took a look at a partial draft, and suggested they do a book just on this event, which is Lucifer's Hammer) it included the aliens, after being driven off Earth once, dropping an asteroid in the Indian Ocean to soften up resistance before trying again.
The aftermath of Operation Oyster Bay in the Honor Harrington series is described in substantial detail, despite being "only" a set of class 0 events.
In Cerberon, the complete destruction of Loethess and everything around it is described in detail from multiple perspectives, from a mage in the center of the city paralyzed with Oh Crap, to a family nearby hoping they'll survive, to a distant overview by a pair of people being carried away by a flying dragon.
That Is All goes through every day of 2012 as it deals with Ragnorak via the awakening of the 700 Ancient and Unspeakable Ones. All the oceans are flooded by a giant sentient pool of blood. All the dogs gather together and eat most of humanity, while the animatronic presidents finish off any remnants. Finally, all the Iron in the world magnetizes, burrowing into the Earth, cutting it in two.
Battlestar Galactica starts with one in both the original and the reimagining. Galactica 1980 starts with a computer simulation of one, and goes downhill from there.
Dollhouse deconstructs its premise to this conclusion: after a season of ridiculously, incredibly Misapplied Phlebotinum, the Season One finale skipped forward10 years and revealed that the Dollhouse's technology would destroy civilization if used just a little bit more creatively.
Shows up in the end of the pilot episode of SGU, and again about halfway through the 19th episode, where both the Icarus-type planets capable of dialing Destiny, end up suffering an Earth-Shattering Kaboom as a result.
In Stargate SG-1, the episode "A Matter of Time" starts with one of a pair of binary stars collapsing into a black hole, while SG-10 desperately scrambles to reach the Stargate in slow-motion... at least, that's how it appears because of the massive time-dilation.
Carter later invokes when she comments they can actually witness spaghettification and the planet being torn appear by the black hole, earning her a rebuke from O'Neill who reminds her that she's talking about watching good men die horribly, in extreme slow-motion.
The Halloween broadcast of The War of the Worlds should be mentioned. An hour long description of Humongous Mecha from another planet destroying everything in their path. Bonus points for making people actually believe it was happening.
As can be seen here,Xenogears does this with Weltall- Id fulfilling its programming and taking out main parts of the superstructure of Solaris. The resulting "reaction weapon" explosion leaves a significant hole in one of the nearby continents on the game map.
The opening of Meteos, involving a number of planets getting obliterated in seconds.
The ending of Mother 3, which features lingering shots of all of the places you've visited crumbling away to nothing. Though the "The End?" screen shows that at least the people somehow managed to survive.
NieR opens up with an intro beginning shortly after the apocalypse hit, with the hero scraping by to support himself and his daughter, fighting off monsters in the process. The game then skips forward thousands of years after the apocalypse, with humanity now struggling to scrape by.
The end of the mission "Shock and Awe" in Call of Duty 4: Modern Warfare, which comes complete with satellite images of the nuclear detonation that kills your character and most of his unit.
A striking point...the people who made the game showed us part of how you would die if you were within about 3 miles of ground zero and not vaped in the blast. Yes folks, expect your death to include barfing your organs out in your last moments on earth to the sound of radioactive wind blowing away the last of your Organ of Corti, that is, the organ that does the actual hearing in your ears.
Things get even worse (or better, in way of trope examples) in the sequel. We see the US East Coast being invaded by the Russians, Washington, DC in ruins, and an EMP occurring over the city wiping out all forms of electronics on the US East Coast!
Darksiders opens with the Biblical Apocalypse. Angels, Demons, the whole shebang. You get to run around and kill things (briefly).
Losing to Lavos in Chrono Trigger will "treat" you to a scene where you see the world getting fried by Lavos's explosive fury. The most iconic scene is watching the viewscreen in the dome fill up with red dots that each represent a big crater, driving the point home that the world is now FUBAR.
In Final Fantasy VI, after Kefka destroys the balance of the Warring Triad, the world is torn asunder. This is depicted as the land shaking, shifting, mountains rising and chasms opening, all while helpless people run for their lives. Then the view changes to a distant view of the planet, covered in hundreds of explosions... and all of a sudden, to drive the point home that everything has changed, a chain of explosions travels across the planet and splits the continents apart.
In Super Metroid, after defeating the Mother Brain and successfully making it back to your ship, the camera zooms out, showing massive cracks in the surface of the planet Zebes, which are apparently even visible from high orbit, before the planet is reduced to space debris. There is a secret sidequest at the end where the last surviving natives of Zebes escape with just moments to spare.
SR-388 in Metroid: Fusion, the Biological Research Laboratory space station plummets into the plant and self-destructs, wiping out both in a titanic Earth-Shattering Kaboom. Planet Phaaze in Metroid Prime: Corruption, with added drama with the Galactic Federation fleet trying to escape in time. Subverted in Metroid Prime: Echoes with the destruction of Dark Aether, we only get a space view of the half-visible Dark Aether fading from Aether.
The aptly named "End of the World" stage in Sonic the Hedgehog (2006). You see some really trippy colors while playing the level as it slowly gets more and more screwed up. Orbs appear as it gets more intense, and then there is a purple glaze that goes over the levels you are playing, until it is a very dark green all over. Somehow, statues with eagles on them can reverse this effect temporarily. It's intense, but for all the wrong reasons. Accompanied with very echoey music which is incredible.
Final Fantasy IX Kuja destroys the entire world of Terra at the end of the third disk. This makes him one of the few FF villains to actually succeed in destroying a world.
Final Fantasy X has (Sin) do this regularly. The fun comes when the rest of the world fights back.
It was taken up to eleven at the conclusion of the game, when Sin was shown punching holes in continents, leaving trails of explosions vissible from space, and releasing gravity magic that made the moon visibly shudder...
The sequel has this as one of the optional endings. Lose the final battle on purpose to see it.
Though hardly appocalyptic, in Final fantasy XII Revenant wings, we get treated to a rare fully animated scene when Bahamut first appears, just in time to show it shattering an entire floating continent, crumbling it almost to nothing....
Freespace 2 ends with the Sathanas Fleet causing Capella to go supernova.
Tiberian Sun's ending of the Nod campaign has Kane teleporting off the world while his Apocalypse missile starts, then launches its capsules and finally unleashes the Tiberium bomb that sets Earth's atmosphere ablaze and turns everything into pure Tiberium.
The ending cutscene (one of only two not rendered using the game's engine) in Assassin's Creed: Revelations shows exactly how the First Civilization was destroyed. There's a Kick the Dog moment with a terrified mother clutching her child as an explosion slowly engulfs them. After this, the hologram simply mentions that out of two civilizations (humans and the First People), only about 10,000 individuals survived after only a few days of the catastrophe.
The Unicron Trilogy version does it a bit differently: he generates sort of a suction that causes a planet to be torn apart as it's pulled toward him. By the time it reaches him, the planet is in chunks small enough to be pulled inside the (relatively) small circle on his body. Ouch◊.
One episode of Captain Planet and the Planeteers ("Planeteers Under Glass") has the Planeteers and a female scientist (Dr. Derek) enter a virtual planet where pollution is sickening the planet in centuries (sped up in minutes), starting from societal disruption up to planetary devastation and species extinction. But then Dr. Blight traps them all in the rapidly wasting virtual planet, bringing the Apocalypse Class up to total extinction and closer to physical annihilation before destroying them all (not even Captain Planet can save them)... or so Blight thinks. Fortunately, the team of Planeteers have a backup spot before they vanish so they can return safely to stop Blight.
Futurama, in "The Late Philip J. Fry": The one-way time machine goes so far into the future that Fry, the Professor, and Bender watch a time-lapse of the end of the universe, complete with stars exploding like fireworks and receding into the distance, while drinking beer and generally treating the events as a spectacle.