Slayers Try has Xellos, who wants the world to be destroyed - but by locals. So when aliens try to do it, he works against them.
Xellos... Oh, Lord of Nightmares, Xellos. How about Slayers: NEXT? The end-of-the-world fails and Xellos was entangled in this all. Complete with him appearing healthy and smiling right after destruction of the strongest Dark Lord who tried to bring it all down. It seems that he and his boss are more interested in power struggles between their kin than in serious apocalyptic activity. And then there's..."My Evil Plan to Save the World" AMV with Xellos.
Majin Tantei Nougami Neuro had Neuro, a demon who feeds on solving mysteries (like solving who killed someone) faces down Sicks, who wants to kill every human because, if every human was dead, who would kill each other and provide mysteries?
While mostly doing anything for amusement, Alucard of Hellsing's stated reason for working for the good guys is that if vampires in general won, they'd eat all the humans, and there wouldn't be any left.
An odd variation in Pokémon: Diamond and Pearl Adventure: Cyrus's plan is to wipe out the universe and create a new, perfect one. When he realizes that the legendary Pokémon he summoned to do it will only destroy everything without the ability to recreate anything, he decides that even a horrifically flawed world is better than no world at all. Basically, he played this trope on himself.
In Pokémon 2000, Ash is bewildered when Team Rocket assists him against the threat. They explain that they are thieves; they have no interest in killing, and definitely don't want the world to be destroyed.
In the final arc of Mobile Suit Gundam Wing, Milliardo Peacecraft plots to destroy Earth out of a misguided belief that the people of the Space Colonies were purer in purpose than those of Earth, who he saw as hopelessly tainted with the specter of the planet's bloody history and could never achieve lasting peace. Among the people arrayed against him is Treize Khushrenada, the leader of OZ, who the protagonists have fought on many occasions. For all his faults, he loves the Earth and does not want to see his people destroyed. It's implied that Treize and Milliardo cooked up the war between them to exhaust humanity's will to fight and demonstrate the foolishness of war once and for all...and it sort of works.
And by, it sort of works, it ends the Earth vs Space Colonies conflict that defines the Gundam Wing Universe. For a couple of months, before another warmongering lunatic starts up a coup right as everyone else was disarming themselves. Naturally.
Dragon Ball Z opens with Alien Invader Raditz coming to find his younger brother Kakarrot and obliterate all life on Earth. Naturally, previous Big Bad Piccolo would rather rule the world himself and as a result teams up with Son Goku to defeat him. This event ultimately leads to him taking a Heel-Face Turn after befriending Goku's son, Gohan, while training to prepare for the arrival of Raditz's even more powerful comrades.
Pretty much any villain in comics who is not specifically an Omnicidal Maniac will step up to help the planet if it's threatened.
Doctor Doom has helped save the world almost as many times as he's tried to conquer it. Notable instances include fighting against Thanos and Onslaught. Plus he pulls a lot of Enemy Mines with Richards against stuff like rogue Celestials or the Over-Mind.
This happens during most of the Crisis Crossover events too. During Crisis on Infinite Earths and Infinite Crisis a wide variety of supervillains attempted to aid the heroes, as the apocalypse was something they all wanted to avoid. Special note should go to the Crime Syndicate in the first Crisis, who die trying to save Earth-3 from the Anti-Monitor, and Darkseid who finally lifts a finger when he realises that the Anti-Monitor threatens Apokolips as well as Earth.
Played with in Les Légendaires; Darkhell gladly tried to help in preventing the reviving of Omnicidal ManiacAnathos on his native world Alysia, but only because this required killing his Arch-Ennemies the Legendaries to ensure Anathos wouldn't reincarnate in one of them; other than that, he could hardly care less about Alysia's fate. Later however, when Anathos still succeeds in coming back, he still helped the Legendaries escape and fight Anathos, even committing a Heroic Sacrifice in the process. This time, it was motivated by his desire to protect his beloved daughter Tenebris.
Lucifer: Fenris the Wolf wants to destroy all Creations. Lucifer wants to save at least his own Creation. Various factions assist and ally with both parties.
In Paperinik New Adventures,The Organization is a group of illegal time-travelers bent on stealing from the past and trying to change it to become the supreme rulers of the future. But when the whole timeline was about to be deleted,they quickly ally with Paperinik to save themselves and their job(they were however planning to doublecross him when the danger was gone).
Inverted in xXx. Xander tells the agent he works for "when you hire somebody to save the world, make sure they like the world the way it is."
The Mummy Returns opposes O'Connell, Imhotep, and the Scorpion King. They are trying to save, conquer, and destroy the world, respectively.
A popular theory about the motivations of the Star WarsEvil Overlord Palpatine is that he wanted to protect the galaxy from the Yuuzhan Vong invasion (and have it for himself, of course).
This may be Lucifer's motivation in The Prophecy for intervening against Gabriel's plan to destroy humanity. He describes Gabriel's dream world as "another Hell," which is one Hell too many for him. Whether Gabriel's world would really be The End of the World as We Know It is not clear, and of course Lucifer could be lying anyway (he's famously good at that), but if we take him at his word, then he is indeed Evil Against Oblivion.
In one novel in Jack Chalker's River of Dancing Gods series, there's a sorcerer plotting to bring about the end of the world. Every other evil sorcerer in the world is against him, once they find out, because they've all done a Deal with the Devil to enhance their power, and consequently want to postpone Judgement Day as long as possible.
Crowley from Good Omens is a demon who rather likes the world and doesn't want the apocalypse to come and ruin everything. In order to avert it, he conspires with Aziraphale, an angel who has spent too much time on Earth and now considers heaven unbearably boring, and wouldn't mind postponing the final battle between good and evil.
In The Dresden Files, Harry often gets help from John Marcone, the crime lord of Chicago. This is because Marcone realizes that if the latest supernatural threat takes over a significant portion of the world, or blows up a large part of Chicago, it would be very bad for business.
Of course, it doesn't hurt that he has a tendency to gain something every time, whether it be the appearance of having a wizard on his payroll, becoming an independent power under the Unseelie Accords, or what have you.
Ghost Story implies that Marcone has actually become Chicago's main defender against the supernatural in the wake of Harry's apparent death.
Lara Raith has sided with Harry against far greater evils for similar reasons, because it's hard to coyly prey upon the human population when it's been decimated.
"Another Fish Story" by Kim Newman, essentially a Villain Episode for his recurring archvillain Derek Leech, has Leech sabotage an attempt to bring about the end of the world — not because he wants to save the world, but because it's unsubtle and uncreative, and his own plan for the end of the world is much better. The stories "Cold Snap" and Seven Stars have Leech forming Enemy Mine alliances with the Diogenes Club for similar reasons.
Villains by Necessity by Eve Forward centres around a group of evil characters trying to stop the world from being destroyed, by unleashing a great darkness to enslave and terrify the land.
"I'm a monster, Miss Cray. But even monsters want to live."
In A Song of Ice and Fire Jon Snow persuades the Night's Watch make a very uneasy alliance with wildlings, giants, King Stannis and Melisandre the Red Priestess/Sorceress in order to prevent the Others from bringing about The End of the World as We Know It. Some characters are sufficiently open-minded about the Grey and Gray Morality of their world to recognize that their allies are not necessarily "evil", but the less even-handed ones who nonetheless accept the alliance do so because of this trope.
Of course, it comes to bite him in the ass when the older, more conservative members of Watch decide he's destroying it and try to kill him.
The Wheel of Time teases this heavily in relations between the various bad guys, though it never actually spills into combat. Ishamael(who was literally a nihilist philosopher before the Big Bad entered the world) does however spend some time mocking the other baddies for thinking that they're fighting for Evil when they're actually working towards Oblivion. This also works between the Forsaken and Padan Fain. While the Dark One's plans for the world are referenced several times in the final book, it actually wants to destroy creation and remake it In Their Own Image in some way, making him and his forces members of "Evil". Fain, over the course of the series, eventually places killing the Dark One and other acts of rampant mass murder on his list of things to do as Mashadar progressively takes over, placing him more in the category of "Oblivion".
In Xenos, the thieves' and assassins' guilds have occasionally aided the Church against servants of the Destroyer, the setting's Satan and Bigger Bad. A leader of the thieves stated that he could ultimately confess his crimes, repent and even seek salvation, but collaborating with the Destroyer would damn his soul for eternity.
Emperor Jagang in The Sword of Truth opposes the Keeper of the Underworld on these grounds: The Keeper wants to unmake the world, whereas Jagang wants to take it over. His primary action against the Keeper is the Mind Rape and enslavement of the Keeper's servants, the Sisters of the Dark.
Buffy the Vampire Slayer, episode "Becoming": Angelus is planning to perform a ritual that will bring about the end of the world. Spike sides with the heroes to stop him, and tells Buffy that under the big talk, a lot of vampires like the Earth just as it is — millions of people running around helpless like "Happy Meals with legs", and a comparative small handful of people who hunt and kill them.
In Doctor Who, the Daleks and most of the Eleventh Doctor's Rogues Gallery concluded an alliance to repair the cracks in the universe. However, this plan backfired spectacularly.
Before that, the serial Logopolis did this with the Master.
Also the Master did the same in The End of Time though it was for more personal reasons.
The Master: *fires electrical blast at Rassilon* "You did this to me! All of my life!" *fires second bolt* "You made me!" "1!" *fires 3rd bolt* "2!" *fires 4th bolt* "3!" *fires 5th bolt* "4!" *fires last bolt*
Heroeshas Sylar. Head-splitting serial killer of specials by day, but would rather not have New York explode since it doesn't fit his agenda. He comes around when he gets a vision of the future where it does fit his agenda.
In season 5, Crowley — a powerful, successful and very evil demon — helps the brothers to combat Lucifer and the world-shattering threat of the Apocalypse, as he's quite enjoying himself.
In season 7 Crowley does this again, as the Leviathans are organizing the wholesale slaughter of mankind, every other monster race besides themselves, and threaten to destroy the demons if they weren't occupied elsewhere. Over the course of the season he subtly aids the Winchesters to find a means to kill the Levi leader and destroy their army.
In season 8 of Stargate SG-1, Ba'al, the last of the Goa'uld System Lords, joins forces with the SGC to keep the Replicators from eating the galaxy. Also later helps out against the Ori. The team gets used to him being willing to do this, but never forgets that he is the bad guy (which he does prove now and again. In fact, the end, he becomes the Big Bad of the final SG-1 movie, having outlived Anubis, the Replicators, and the Ori mostly by being Dangerously Genre Savvy.
Cyrus Crabbe in the Dinotopia TV movie joins with the Scott brothers to save the island from the rampaging pteranodons, even though he hates the Dinotopian way of life and wants to leave.
Crabbe: Don't you get it? I'm trying to save this hell of a place. Not 'cause I like it, but 'cause I'm trying to save me own skin.
Probably the reason why Set, the fratricidal god of chaos in Egyptian Mythology, helps Ra to slay the serpent Apep. After all there would be no world worth ruling if the sun and heavens were destroyed.
Hilariously inverted in Planescape. Shiva peacefully sits in the big vortex on Negative Energy Plane and presumably (it's not like even planars can be trusted in such matters) contemplates his role in the destruction of the Multiverse — when its time will come, that is. Every once in a while someone stumbles on the same bright idea: "Hey, maybe this guy does requests?" and visits him to check. As far as anyone knows, these supplicants just go in and never return.
In "The Plane Below" for fourth edition it goes into the psychology of Archons. Created by the Primordials to wage war on the non-elemental creatures that served the Gods, they still exist and still regularly attack and kill non-elementals. However, they need battle and slaughter like humans need shelter and companionship, so they stop just short of pure genocidal mayhem. If they ever actually destroyed every other creature, then they wouldn't have anything to fight anymore.
This is true in Legend of the Five Rings. The Sleeping Void is seen as not being truly evil, because it simply wants to end everything, while the forces of the Shadowland ARE evil, and want to conquer the world.
In Nomine, by Steve Jackson Games, has a few instances where Heaven and Hell have come together to destroy a rogue Demon Prince who attempted global devastation. Most notorious was Legion, the second Prince of Corruption, but the Prince of Pestilence, who kicked off the Black Plague, had to be taken down as well.
The Seers of the Throne from Mage: The Awakening have "maintain the Abyss" as one of their commandments. "Maintain" is the key word in that phrase — the Seers keep humanity fractious and miserable to prevent them from Awakening. They do not take kindly to people like the Scelesti actively serving the Abyss, and a Scelestus is one of the few things the Seers and the Pentacle Orders will work together against.
There's also a slight inversion when it comes to the Lower Depths, which count the Inferno amongst their number. In one fiction piece, a Scelestus argues to his interrogator that at least the Abyss just wants to annihilate reality; the dwellers of the Inferno want to make it bleed.
Similarly, in Mage: The Ascension, the Technocracy distrusts the Traditions but recognizes that the Nephandi are far worse.
In Exalted, we have the Neverborn, the tormented, undead remnants of the murdered Primordials; the Deathlords, ancient and powerful ghosts sworn into their service; and the Abyssal Exalted they corrupted from stolen Solar shards, all of whom want to drop Creation into the Well of Oblivion. Absolutely no one else wants this to happen, including the other "bad guy" factions, such as The Fair Folk and the Infernal Exalted. Even the Ebon Dragon, the personification of evil, cruelty, treachery, and general bastardry, opposes them, if only because nonexistence would put a severe crimp in his plans to bring about eternal suffering and torment. note Note that the Dragon inverts the usual Eviler than Thou arrangement - one supplement specifically notes that, horrible and nihilistic though it would be, the utter extinguishing of all Creation would be better for everyone than letting the Ebon Dragon remake it in his image.
Aforementioned Fair Folk have their own variation on the theme - some of them want to unmake the world back into Pure Chaos in which they will continue to play their games for eternity, while the others like the tasty mortal souls too much to just kill them all at once. (They both wouldn't like the Oblivion of the Neverborn of course.)
In Magic: The Gathering, even the most selfish planeswalkers (godlike multiverse-travelling mages) sometimes help the good guys to thwart something even more horrible.
In the Zendikar and Innistrad storylines, the planeswalker Sorin Markov is not exactly a nice guy, being an arrogant, hedonistic vampire who goes around eating people and so forth. But even he had the decency to go out of his way (even risked his life?) to prevent Eldritch Abominations, demons, and other vampires from depopulating entire planes of all intelligent life.
In the Time Spiral storyline Nicol Bolas, an Elder Dragon planeswalker and one of the oldest and most evil characters in the game, actually offered some help in preventing the time rifts from destroying the whole multiverse. Not that he stooped to sacrificing his own planeswalker spark to do so; he killed Leshrac and used his instead. Then again, Nicol Bolas is also the bastard who mucked up Sorin's plans and let the plane-eating Eldrazi loose again, for no particularly discernible reason. Jerk.
In the multiplayer format Archenemy has players take the role of planeswalkers forced into alliance against another planeswalker who is about to set in motion some world destroying magic. Archenemy deck names included "Bring About the Undead Apocalypse" "Trample Civilization Under Foot", and "Assemble the Doomsday Machine".
Nobilis presents us with the Imperators and the Excrucians. The former include Angels, Demons, Aaron'sSerpents, Wildlords, Lords of the Light and Dark, and a smattering of other god-like entities, all of whom tend to follow Blue and Orange Morality. The Nobles, their semidivine servants (which includes the Player Characters), are human enough that they can be nicer than their bosses, but also human enough that their malice can arise from genuine sadism rather than disinterest or ignorance. Not exactly a nice bunch, but at least they're a better group than the Excrucians, who want to unmake reality to the point of it never having existed in the first place. They've already succeeded in part, but the extent of that success is by nature unknown and unknowable.
Pathfinder has the Lawful Evil devils and Chaotic Evil demons; the former want to crush the universe under their heel and the latter want to corrupt and destroy everything they can, but neither really want to kill every living thing; that's the Neutral Evil daemons' goal. They all tend to clash together thanks to their rather mutually exclusive goals.
Also, in the lore, the Lawful Evil god Asmodeus (who is modeled largely on Satan) aided the good gods against Rovagug, the Chaotic Evil god of destruction. When Rovagug was imprisoned by the other gods, it was Asmodeus who made the lock.
The World Ends with You: The Big Bad, Megumi Kitaniji, is actually in a game with the Composer to decide the fate of Shibuya. Neku happens to be playing for the Destroy Shibuya team.
In Sacrifice, there's a prophecy that one of the gods is going to bring about the end of the world, and suspicion immediately falls on Charnel, the god of death and suffering. He denies it, pointing out that if the world ends, there will be no people left to suffer and die, so it's in his interest to keep the world as it is.
Bowser from Super Mario Bros. does this sometimes, when he doesn't accidentally destroy the universe himself. Most prominently used in Super Paper Mario where he's actually playable and fulfills a role in the prophetic group of heroes. Bowser also still is the King Koopa, and if something threatens his subjects or his reign, he'll try to stop it. Pointed out further in Mario & Luigi: Bowser's Inside Story; Dark Bowser wants to destroy the kingdom, but Bowser will have none of that, otherwise there won't be a kingdom for him to rule.
Similarly, most of the mainline 3D Sonic the Hedgehog games generally end up with this conflict as justification for Dr. Eggman fighting alongside the heroes against some ultimate evil in the True Ending, usually one that he released himself. It started in Sonic Adventure 2, and the trend wasn't really bucked until Sonic Unleashed (where Eggman really couldn't care less what Dark Gaia was up to, as long as he could harness the thing's power for his own) and Sonic Colors (where Eggman is the ultimate Big Bad). Sonic Generations plays with it, as Time Eater captures Eggman no less than twice throughout the game, seemingly against both parties. Except that both Classic and Modern Eggman control Time Eater; these were actually elaborate escape plans to throw Sonic off their trail.
Inverted in Mastermind World Conqueror: the Mastermind apparently believes that conquering the Earth and blowing it up are in fact the same thing (he looked it up).
The "Earth Defenders" (IE: Godzilla, Mothra, Rodan, Anguirus, Baragon, King Seesar, and Varan) in Godzilla Unleashed fall under this. While most of them couldn't care less about what happens to humanity in particular, they are more than willing to protect the earth (hence their title) from any threat that wants to destroy it.
From the main series, Emperor Gestahl of Final Fantasy VI objects to Kefka assuming supreme magical power because then there wouldn't be much of a world left to rule afterwards.
Similarly, the Shinra Corporation in Final Fantasy VII wants to stop Sephiroth just as much as the protagonists do. Too bad their incompatible methods mean teaming up isn't an option. Especially since Shinra's plan to thwart Sephiroth wouldn't actually have worked even if the heroes hadn't interfered.
Halo has an odd example of what could be considered oblivion vs oblivion. The Gravemind wants to consume all life in the galaxy, leaving nothing but a pestilent mass of Flood, while the Prophet of Truth wants to activate the Halo rings and thus wipe out all organic life in the galaxy (under the mistaken impression that it will ascend him and his followers to a higher plane of existence, which in reality is an incredibly determined effort to prevent the revelation of the fact that the Covenant's entire religion was a lie). If you factor in 343 Guilty Spark (who has the same goal as Truth, but for wholly different reasons) then you have an unprecedented 3-way war in which each side wants to destroy the galaxy.
Which in Halo 3 results in a truce between Humanity, the Covenant Separatists, 343 Guilty Spark, the Ark's army of Sentinels, and for a very brief period of time, 'the Flood, all just to stop Truth from firing the Halo Array. The Flood go back to fighting everyone and everything immediately after Truth is killed, and Spark goes rampant and ends up killed by the Chief, with the Sentinels following suit.
Cerberus in Mass Effect 2: they're a human supremacist organization that, just this once, isn't going to complain about working with alien allies. Why? If the Reapers wipe out the galaxy, that's obviously not in humanity's best interests, and The Illusive Man is smart enough to know that humanity cannot defeat the Reapers on its own. Then they go ahead and get indoctrinated in Mass Effect 3 and wind up fighting more or less on the Reapers' side.
In Mass Effect 3, the crime lord Aria T'Loak is willing to cooperate and send a massive fleet of mercenaries and criminals to aid in the fight against the Reapers. After all, can't live a profitable life of ruling the Wretched Hive of Omega if the Reapers kill everyone, right?
City of Villains has a few storylines where you, an aspiring supervillain, get to save the world. This is also the justification for teaming up with heroes in the end-game "incarnate" content.
There's also a badge for heroes who do a specific mission called "Saved the world". If you become a villain (via the morality system), the name of the badge changes to "Saved the world... for later"
DC Universe Online shows the obvious problem for villains having this attitude: Lex has to time-travel to find the Justice League to help him save the world. Because previously, he won against the League. So if you don't want oblivion, villains, maybe you shouldn't try to kill the heroes at all.
In Star Wars: The Old Republic, one of the Sith Emperor's top enforcers joins with the Hero of Tython (the Jedi Knight Player Character) to stop the Emperor from consuming all life in the galaxy. In the games's backstory, he had worked with Revan and the Jedi Exile with the same goal, only to turn on them when he had a vision revealing the Hero of Tython as the one who would stop the Emperor – that betrayal earned him his position and the long life that ensured he would still be around to later work with the Hero.
In God of War, you are playing for the oblivion side. Kratos destroys another part of the world with each god he slays in GOWIII. The gods are fighting to preserve the world. By the end of the game civilization, the order of nature including the afterlife, and nearly all if not all of the entire human race is gone. Even the "evilness" of the gods is questionable. They could be major jerks to humans, but only became truly evil after being infected with the evils from Pandora's Box.
The Guardians in OFF may be huge Jerkasses and Bad Bosses with little regard for the Elsens they rule over, but in they end they end up fighting to try and save their respective Zones from the Batter purifying them, which would erase everything.
In Portal 2, this is the motivation of GLaDOS for helping Chell stop Wheatley; his incompetence will inevitably result in the destruction of the Aperture Science facility.
Xykon: I like the world. Some of my best evilness took place here. I wouldn't mind ruling it, in fact. I'm certainly not about to destroy it unless I get really, really bored.
His Dragon, Redcloak, walks the line. The plan is to give his god, the Dark One, the ability to unleash the Snarl at will to threaten the other gods into giving goblins a better lot in life. Though if things go south and the Snarl winds up destroying the world (again), the Dark One will get a say in how the next world is created, ensuring that the goblins of that world get a better deal. So whether Evil or Oblivion wins, so does the Dark One.
Later, Tarquin promises to help Elan, despite being on opposite ends of the alignment scale, precisely because he knows Elan is on a quest to save the world and, as the power behind the throne of a good sized kingdom, he has a vested interest in seeing that happen.
When Durkon is turned into a vampire and thus goes from Lawful Good to Lawful Evil, he continues fighting alongside his mostly-good team. Regardless of his alignment, he has no desire to see the world end.
Kid Radd has three villains. Crystal wants to conquer the world, in revenge for the wrongs she has endured. GI Guy wants to destroy the world, out of despair after two failed utopias. The Seer wants to conquer the world then destroy it before moving to the next planet and repeat the process, because that's what a Computer Virus does (with a dose of sadism too). Their actions indirectly serve or complicate each other's plans.
Atop the Fourth Wall has Lord Vyce and The Entity. The former claims he started as a genuine hero, merely warning alternate realities of the danger they were in, but became a ruthless Multiversal Conqueror after everything else failed. Also, Doctor Insano is not only willing to call a truce, but even ignore Linkara stealing his prized deathbot in order to defend the stability of hypertime.
Happens in the backstory of Reflets d'Acide when the Demon Lord Bélial shew up for the first time. His arrival resulted in Evil Overlord Alkor joining force with King MageMaender, presumably for this reason. Notably, it seems the alliance actually survives after Belial was defeated.
This regularly happens in Worm, where giant Kaiju with ruinous superpowers known as the Endbringers regularly emerge from the ocean, the center of the earth, and the upper atmosphere, select a target (usually heavily populated or otherwise vital) and proceed to do their absolute best to wipe it off the face of the planet. It's common, codified practice for superheroes and supervillains to join forces against them, because the Endbringers are doing a very good job of slowly wiping out humanity and the majority of supervillains simply aren't that evil.
Likewise, it justifies Thou Shalt Not Kill on both sides of the equation; the more powerful and troublesome a hero is for the villains, the more needed he tends to be against the giant monsters. One character describes the normal interactions between heroes and villains as "like a big game of cops and robbers."
Dr. Arkeville from the Transformers multi-parter "The Ultimate Doom" helped the Decepticons with a mind-control plot, in exchange for world domination, until he found out the ultimate goal would leave the earth a lifeless husk.
Arkeville: I will be ruler of a dead world!! Megatron: A simple problem, Doctor, for such a brilliant mind.
In later incarnations of the metaseries, Megatron (or, for more unhinged Megatrons, the more sane evil Decepticons) will at least try to team up with the Autobots to combat Unicron for "if he eats it I can't rule" reasons. It almost never works out for Megatron and he ends up doing Unicron's bidding semi-against his will, but its the thought that counts.
He does rather better at resisting Unicron's control in Transformers Prime, and directly aids the Autobots in defeating him so that "this time, there will be a planet left for me to rule!"
In Spider-Man: The Animated Series the Kingpin places his considerable resources at Spider-Man's disposal when the Spot's technology threatens to destroy the planet. In his own words "There is no profit in the end of the world."
In "Planet Jackers", an episode of Invader Zim, another race of aliens steals the earth in a Dyson Sphere intending to use it like firewood to keep their sun alive. Zim immediately decides he has to stop them since if they do this, he can't be the one to destroy the earth.
Averted in Justice League: Doom: Vandal Savage's plan for conquering the world involves not simply murdering the Justice League, but also destroying all electronic technology ("anything more advanced than the steam engine," he says) and killing at least a third of the world's population outright. You'd think that at least Metallo and Mirror Master would object to the former, and it's hard to imagine that Star Sapphire is bad enough to countenance the planned apocalypse.
The finale of Danny Phantom has all the recurring ghost villains help Danny save the world from a meteor. Not entirely altruistic, though: the Ghost Zone is tied to the Earth, so the ghosts will share Earth's fate should the meteor hit.
Chase Young, Wuya, and Jack Spicer in Xiaolin Showdown, prompting them to join forces with the Xiaolin Warriors on a couple of occasions. Here it's definitely of the "if the world is destroyed then I can't rule it" variety.
When Chrell begins erasing the TMNT multiverse in Turtles Forever, several villains turn against him. For a moment, it looks like it will culminate in a fight between him and Krang, as giants, but the latter is quickly defeated.
In Darkwing Duck, Megavolt teams up with the gang after accidently "galvanizing" Negaduck and turning him into a Person of Mass Destruction. They ask why he'd help them, and he says that if Negaduck destroys St. Canard, there'll be nothing left to rob.
Played straight in Justice League: Crisis on Two Earths: When the Crime Syndicate learns that one of their members plans to destroy all of creation, Johnny Quick instantly volunteers to help stop it, saying that his world is in jeopardy too.
The season 3 Series Fauxnale of Johnny Test has Johnny enter an Enemy Mine situation with several of his nemeses to stop Dark Vegan from destroying all life on Earth, arguing that they want to take over the world and can't do that if there's no world.
The Batman episode "The Joining" has the inmates of Arkham Asylum and the G.C.P.D. fighting off the aliens side-by-side. The Joker even makes a direct reference to the trope after watching Mr. Freeze and Commissioner Gordon covering each other.
Xanatos sometimes takes the "evil" side against Demona standing in for "oblivion" in Gargoyles. Now, Demona doesn't want to destroy everything, but she does want to wipe out the human race (which as far as those of us who belong to the human race are concerned amounts more-or-less to the same thing), something the largely amoral Xanatos's sense of self-interest and self-preservation is far too strong to allownote Xanatos wants money, power, and immortality. As of the show proper, he has the first two and is busy using them to try and get the third. The end of the world- or of humanity- would put an obvious crimp in his plans. To give some specific examples, he pulls a straight up Enemy Mine with the clan in "City of Stone", and though he doesn't show up in Hunter's Moon until the battle is already won, he's certainly grateful enough that humanity is saved to provide a very timely airlift out of trouble.