Lone Wolf and Cub has Retsudo Yagyu and Abe-no-Kaii Tanoshi. Kaii attempts to destroy both Yagyu and the main character, Ogami Itto, while Retsudo spies on Kaii with plans to kill him after Itto. Eventually, Retsudo gets fed up with Kaii and frames him for a seppuku-worthy crime. Kaii dies.
Pokémon: Teams Magma and Aqua as always, and Teams Rocket and Plasma as well.
Excel♥Saga. One side is World Domination group ACROSS, trying to take over Fukuoka City as a first step towards taking over the world. The other side is the very corrupt Department of City Security, trying to stop ACROSS. Both recklessly disregard the lives of the people living in Fukuoka in their attempts to take the other one down.
In Haruhi Suzumiya, Ryoko is extremely forward about her plans. She wants to kill Kyon in order to provoke a massive data explosion from Haruhi. Admittedly, this could cause the end of the world, depending on how much Haruhi loves Kyon. Yuki stops her and deletes her. Fast forward to nine novels later. Yuki is sick. ( She's become ambassador to the Sky Canopy Dominion, because they aren't allowed to kill her after Kyon's threat. Next best thing is to send her to Cthulhu, and hope that'll break her completely.). Just when Suyoh comes out, and attacks Kyon, Ryoko arrives, in a Big Damn Heroes arrival, and protects Kyon. She still wants to kill him, but for now, only she can kill him.
Kimidori: Your potential usefulness was marginally greater than the threat you present.
Mayuri Kurotsuchi (who is technically still evil) achieves his Big Damn Heroes moment when he saves Ishida and Renji from Szayel Aporro Granz, who was gleefully torturing them by snapping every bone and tendon in their bodies one by one.
Kenpachi Zaraki, Blood Knight galore, versus Nnoitra Gilga, a He-Man Woman Hater. While Kenpachi just fights for the sake of getting a thrill out of it, he has his own code of honor, like not killing weaker enemies, and he has a(n equally battle-hungry) Morality Pet. On the other hand, Nnoitra fights dirty, attacks wounded opponents, mistreats his own subordinate, kicks a child in the gut, and practically tortures The Hero throughout their fight.
Kekkaishi is oddly getting to be like this. Aside from the guardians of Karasumori, there are two main factions. Sousui is attempting to bring down the Urukai, and Shinyuuchi-hunting. Yumeji is attempting to stop the former, but is also Shinyuuchi-hunting and trying to destroy Karasumori. (For those unfamiliar with the series, Shinyuuchi-hunting is the act of killing a god and taking over its domain. Considered to be the ultimate perversion of the laws of nature.)
The most literal example is probably the fight in the Flying Pussyfoot between the Lemures and Ladd's gang. The Lemures are a Cult devoted to the immortal Mad Scientist Huey Laforet and they plan on slaughtering the passengers as a sacrifice to their leader/show of force to free their leader from prison. Ladd's gang are a bunch of psychos who are there to hold the train for ransom...after killing half of the passengers. Ladd's gang only kill the Lemures and by extension rescue the passengers, because they want to kill the passengers themselves, purely For the Evulz.
The presence of the Rail Tracer makes this a three-way bad guy fight.
Gundam also used it a few times. Zeta Gundam featured the first three-way of the series with the Titans fighting with Haman Karn's Neo Zeon, followed by the infighting of the Glemmy faction versus the Haman faction in Gundam Double Zeta.
Gundam Wing starts out OZ vs the Earth Sphere Alliance, then the Treize Faction (of OZ) vs (Romafeller Foundation) OZ, then the White Fang vs OZ.
After delving deep enough into the plot of Mobile Suit Gundam Age, it's evident that the war between Earth Federation and the Unknown Enemy is this.
In One Piece, the Seven Warlords of the Sea, the World Government'sToken Evil Teammate serve as this, going after other Pirate crews, who are all viewed as evil by the WG and Marines, and who are almost all not good like the Straw Hat crew. In a way, this sort-of sums up the Pirates versus the World Government. Especially when you have people like Fleet Admiral Akainu and Vice Admiral Onigumo in such high positions in their armed wing, or a guy like Rob Lucci as the leader of your top assassin squad. And whether Dragon's Revolutionaries are actually good remains to be seen. Bartholomew Kuma used to be a member before becoming a Warlord, after all, and he's said to have been a vicious mass murderer (although his actions prior to losing his free will to his cyborg conversion make him look like one of the more decent of the Seven Warlords, so it's not clear-cut in any case).
Invoked in Basilisk by the Shogun, to head off another Evil Versus Evil Xanatos Speed Chess occurring between the nannies of his heirs, and remove them from influence over the succession.
Happens to some extent at the end of the first season of the Black Butler anime. A psycho Fallen Angel tries to burn London to the ground as the first stage of an attempt to "purify" humanity. Humanity's only hope ends up being a demon who, for various reasons, wants said angel dead.
The second season initially appeared to be leading towards this type of conflict, but very quickly abandoned this approach by having Claude, previously morally ambiguous a la Sebastian, off Alois, briskly setting him up as the main antagonist and effectively eliminating the moral ambiguity aspect.
The whole principle of Ciel's role as the Queen's watchdog is like this. Ciel achieves the Queen's desires and keeps stability through many times evil means. It is not too surprising that a police officer calls the Earl a demon.
Fullmetal Alchemist pits Greed against the other homunculi and Father. He betrayed his creator and "siblings", and remains against them right up to his death.
Al: That makes you a friend of Envy, Lust and the others, doesn't it?
Greed: I wouldn't say 'friend'; more like 'sworn enemies' if you wanna get down to the grit.
Liar Game is more of a down to earth type of story but it goes on and on for chapters on Round 4 where Yokoya and Harimoto are competing with each other, and in times making alliances even, to a point that our main heroes, Akiyama and Nao, kinda disappear. Even Yokoya and Harimoto kinda disregard Akiyama as a threat for a while. Big Mistake.
Black Lagoon has an awful lot of this going on. With very few exceptions it's extremely hard to see what, if anything, distinguishes the protagonists and antagonists on a moral level. Possibly nothing, except for the strength of the person's Freudian Excuse. In Black Lagoon you're either a mafia leader or a complete psychopath. Or both.
Yu-Gi-Oh! has a duel between Yami Marik, a psychopath who likes to Mind Rape and attempt to murder people, and Yami Bakura, a thief and murderer who wants the Millenium Items for his own mysterious reasons. The chapter/volume this duel appears is actually called "Evil VS Evil", making it an intended example of this trope. We're meant to be rooting for Bakura, as he's got Marik's good half on his side... too bad he loses. It has the honour of being both this and an example of Ham-to-Ham Combat— it becomes the kind of duel that needs to be seen to be believed.
Yami Yugi versus all the villains in season 0.
In the various Slayers series, the Mazoku Race shows up to be exemplars of this trope on a regular basis, usually through Xellos. The main plot Arc of Slayers Try is an archetypical example of this trope.
In Naruto you have Sasuke vs. Danzo. The former is planning to kill everyone in Konoha to avenge his clan, while the latter was responsible for said clan's demise, along with many other questionable deeds, including trying to let Konoha get destroyed just so he can take it over.
Sasuke does this quite a bit; he also fights Deidara, a terrorist whose "reason" for fighting is literally "just because", and Orochimaru, an Evil Overlord who also tried to destroy Konoha and has virtually no regard for the lives of anyone except himself.
In the backstory, there's Pain/Nagato vs. Hanzo. Hanzo was a paranoid warlord responsible for the death of Nagato's best friend, which makes Nagato jump off the deep end; after killing Hanzo, he murders everyone even slightly associated with the warlord, declares himself a god, and forms a terrorist organization with the aim of enforcing world peace through the series's equivalent of a nuke.Only a few brief verbal descriptions and a handful of flashback panels allude to what surely was an epic war. The anime gives Adaptation Expansion a go and really dives into the meat of the war.
Naruto himself dives into evil territory when he's being controlled by the Nine-Tailed Fox sealed inside of him; he's faced both Orochimaru and Pain in this state.
During the Saiyan Saga, Vegeta and Nappa, two murderous Blood Knights, depose an Evil Overlord on the planet of Arlia after he made the mistake of locking them both up. The people think they've been saved from an evil tyrant, only for Vegeta to remind them that he's a villain as well when he blows up the planet for shits and giggles.
The Namek saga has Vegeta almost in the role of Villain Protagonist. He is the Big Bad of the previous arc (barely a month before), and that his methods for obtaining Dragon Balls (devastate the village it is kept) are exactly the same that Frieza and his men employ. But, with Goku in space/healing and Piccolo dead, he is the best chance of holding off or defeating Frieza for most of the saga.
In Holyland, Katou tries to muscle in on King's drug operation. It does not end well for him.
Hellsing's final battle turns into something like this after most of London's civilians have been slaughtered. On one side there's literal Knight Templars with orders to kill any Protestants, and on the other are baby-chomping vampire Nazis. And finally there's Alucard.
In Futari wa Pretty Cure, the fact that the Dark King and the three Dark Seeds didn't get along was the only reason the girls stood a chance. Ridiculous levels of power were being thrown about in the last few episodes... but thankfully not at them at the time they were least able to fight back.
Black Joke features zero good guys, with all important characters being organized criminals.
The quintessential comic book example: Wanted, the story of the son of one of the world's most skilled supervillains in a world where a much, much more grotesque, inhuman villain is waging war with — yes — other supervillains, for control of the world, which has fallen under the control of — hey, you guessed it! — supervillainy.
The DCU has the Suicide Squad, a US government black ops unit made up primarily with jailed supervillains who agree to undertake dangerous missions against other supervillains with promised clemency if they survive.
The Larry Hama-written G.I. Joe comics by Marvel had the Cobra Civil War storyline, where Serpentor and the Crimson Guardsman masquerading as Cobra Commander fought over control of Cobra. Destro and his Iron Grenadiers represented a third villain faction in the conflict. The Joes didn't have much to do but bear witness to events though Serpentor's faction had bought their support from corrupt elements within the Pentagon.
The revival comic also had a storyline or three about Cobra factions gunning for each other, including one named... Cobra Civil War.
Even though it was called Super-Villain Team Up, Marvel's comic series featured Namor and Doctor Doom (Namor being an Anti-Hero of sort during those days. And yes, nowadays again as well.) fighting mostly each other and other supervillains. Only the occasional hero would show up and get involved.
The DC crossover event Reign in Hell pitted the half-demon children of Shazam, Blaze and Satanus, against Neron (who was retconned into being the ruler of Hell instead of being just another demon lord) in a bid to control all of Hell. A few of the magic-using DC heroes got involved in the conflict because the fallout of the infernal struggle was screwing up magic in general. It ultimately ended with Satanus defeating Neron by transforming all the demons of Hell into humans (which had the side effect of stripping Neron of most of his power that was absorbed from other demons over the millenia), Neron's head on a pike, and Blaze betraying Satanus in a moment of weakness making her the new Queen of Hell.
Geoff Johns' Rogue War, which pitted two teams of The Flash's rogues (one led by Captain Cold, the other by the original Trickster) going up against each other, (over the body of Captain Boomerang, among other things) soon joined by a third group (brought together by the Top). This leads up to a CMOA where Captain Cold, almost the epitome of Even Evil Has Standards, freezes then kills the Top, the whole time berating him why this shouldn't have happened.
Captain Cold: Forgot one of the rules, Top. Rogues shouldn't fight each other. 'Cause when they do... *shatters the frozen Top* bad things happen.
In the Marvel UK Transformers Generation 1 story "Target: 2006", Galvatron travels back in time and kicks everybody's arses, trapping Megatron and Soundwave under a pile of rocks. With the Autobots badly beaten, Ironhide decides to free Megatron in a desperate bid to defeat Galvatron. Oh, and while that's going on, Starscream is acting against them both.
Happens a lot in the comics, actually. Shockwave frequently faced off against Megatron; Starscream manipulates Scorponok and Ratbat into sending their respective armies into combat in the Underbase Saga; Jhaixus kicks Megatron's arse in Transformers Generation 2 to solidify his position as the real Big Bad of the storyline; etc.
The Secret Six. Balancing them fighting bad guys with occasional suggestions of just how brutal they really are is a large part of the series.
One Spider-Man issue featured Electro getting the security blueprints of the banks he planned to rob from a crooked sales representative. Unfortunately, the representative was selling Electro out to the Shocker, who would get to the banks before Electro did and empty the vault. When Electro realizes that he's being double-crossed, he goes back to the crooked sales rep with the intention of frying him, only for the Shocker to interrupt and save the sales rep. Electro and the Shocker then fight for all the loot they both intended to steal. Electro wins.
The presidential election in Transmetropolitan. The incumbent, the Beast, is a Richard NixonExpy who firmly believes that he has done his job if, at the end of the day, a majority of his constituents are still alive, and whose major accomplishments in office consist of abusing his powers to punish demographics that support his opponents and getting the Supreme Court to rule that campaign contributions are personal gifts. Over in the Opposition, meanwhile, the race for the nomination has come down to two men: Bob Heller, who would be A Nazi by Any Other Name if the characters didn't keep openly referring to him as a Nazi, and Gary Callahan, who confides to the protagonist that he wants to be President For the Evulz. In the end, Callahan cuts a backroom deal with Heller to win the nomination, goes on to defeat the Beast, and becomes a poster boy for President Evil.
Boom Studio's French import7 Psychopaths chronicled a group of army-sanctioned crazies who are trained and parachuted into Germany to kill Adolf Hitler. The group included a sociopathic mimic, a bloodthirsty maniac who shrugged off pain, a man who believed Hitler to be an actual demon, and a mother with impeccable sniper skills.
In Forever Evil, it's Lex Luthor and his Legion of Doom against the Crime Syndicate. This is also present in the side stories — Rogues Rebellion features the Flash's enemies the Rogues fighting against the Crime Syndicate's forces, while Arkham War features the inmates of Arkham Asylum (led by Scarecrow) fighting the prisoners of Blackgate (led by Bane) fighting for control of Gotham.
During the events of Last Son, General Zod and his army manage to take over most of Metropolis. Superman recruits Luthor and the Superman Revenge Squad (composed of Bizarro, Metallo, and Parasite) to take Zod on. It works, largely because Zod and his men don't know Superman's enemies, and therefore have no idea that they shouldn't get close to Parasite, that the pretty green rock in Metallo's chest is lethal to them, or that Luthor is far smarter than any of them.
MAD's Spy vs. Spy, in all its various incarnations. Except for their arbitrarily assigned color scheme, the two sides are identical, committing the same horrible (if hilarious) atrocities on each other. (Which was creator Antonio Prohias's whole point.)
In Harry Potter and the Methods of Rationality Draco believes (along most Slytherins, apparently) that Dumbledore was the Greater Evil and that Voldemort and his Death Eaters, though bad, were the only people with a chance to stand up to him.
During the last third of the Digimon story Zero 2 A Revision, UmbraDevimon and Demon both invade the Real World at the same time; apparently deciding that it's not big enough for both of them, they start throwing their armies at each other in order to wipe each other out. And then, the Gravemon invade as well, and they suddenly find something more dangerous to worry about.
This has popped up a couple of times so far in Queen Of All Oni: First, Valmont used the first Oni mask to steal control of the Ninja Shadowkhan away from Jade and turned on her, forcing her into a brief Enemy Mine with Jackie. Then Ikazuki showed up and, after a brief fight, forced Jade to serve him, at least until the J-Team defeated him. And seeing as Jade's ultimate plan is to overthrow Tarakudo as ruler of the Oni, this will probably show up some more.
In a situation not involving the Oni, Jade gets captures by the Evil Sorcerer Lung, who wishes to break her to his will, thus granting him control over her and her tribe. Jade's minions, Left and Right, track him down and launch an assault on his fortress, completely curb stomping his forces before fighting and killing him and freeing Jade.
And then there's Drago, who comes back in time to eliminate all rivals to his power in the future, including Jade. Because of this, the Matriarch (Jade's future self) sends her servant Karasu back in time after him to stop him. Meanwhile, Drago also ends up fighting present-day Jade's foreman Blankman.
There's also the Shadow Hand fighting the various creatures sealed in the Vault of Endless Night.
Narrowly subverted in the Pony POV Series. Discord's mind games drive Princess Luna nearly to the point of turning back into Nightmare Moon to stop him. She just barely restrains herself enough to regain her grasp on sanity, but still assumes her Nightmare Moon form in order to trick him. Also subverted later, as many assumed the second Big BadPrincess Gaia/Nightmare Whisper would overlap and fight with Discord upon his release, but that wasn't the case.
Played straight in the Epilogue/Dark World timeline — about five hundred years prior to the "present" of the Dark World arc, Grogar escaped from his imprisonment and went to war with Discord for control of Equestria (given their respective M.O.s, this is also an all evil version of Order Versus Chaos). Notably, during the war many of Discord's enemies allied with Grogar, as they viewed his "perfect order" as preferable to Discord's "perfect chaos". Sadly, Discord ended up winning, condemning Equestria to a further five hundred years of his rule. Though this might be a good thing, as Word of God has stated Grogar in this timeline is a monster in his own right and essentially a DarkseidExpy.
Queen Cocoon vs Chrysalis in Chrysalis' Origins Episode. While Cocoon did make Chrysalis a slave and was in general a terrible ruler who almost destroyed the changelings by pure incompetence, Chrysalis was still a budding Sociopath with a considerable body count by that point in time. Chrysalis even says she's not opposing Cocoon because Even Evil Has Standards, but because she's disgusted with Cocoon's incompetence.
Flashbacks in the Wedding Arc reveal another example: Chrysalis vs General-Admiral Makarov, who tried to kill her for no reason other than to satisfy his ego. And given that both were created by Pandora, this also counts as an all evil version of Cain and Abel.
The Immortal Game: Titan and Discord have been enemies for thousands of years, and prior to the former being sealed away by the Princesses, constantly fought over control of Equestria. The desperate heroes exploit this to recruit Discord into an Enemy Mine.
The premise of The Cadanceverse is that both Celestia and Luna were corrupted (becoming Burning Sun and Nightmare Moon, respectfully) and eventually waged war on each other, forcing Cadance to seal them both away. They eventually get loose in the present (in the first fic of the series) and go right back to fighting each other for dominance. Though, once they realize that the Musical 6 are on the verge of retrieving the Elements of Harmony to use on them, they briefly team up to destroy them (they both lose).
Freddy vs. Jason - Freddy Krueger from A Nightmare on Elm Street is pitted against Jason Voorhees from Friday the 13th. Both are mass-murdering serial killers. The winner is fuzzy, but on the whole most people find themselves siding with the guy who isn't a child molester (even if he does have many, many more kills). Even the heroes end up rooting for Jason over Freddy because they decide Jason is the Lesser of Two Evils between them. There was also a pragmatic reason for the protagonists supporting Jason over Freddy. While Jason may have had a bigger body count, he's generally less dangerous because he tends to stay in Camp Crystal Lake unless provoked. Freddy actively hunts for victims and can kill you anywhere in the world as long as you're asleep.
Jackie Brown: A crooked Air Hostess who has no qualms about holding people at gunpoint, working for gun smugglers and betraying people left, right and centre is the good guy, next to the gun smuggler himself.
The premise behind Payback. After being betrayed and shot multiple times, ruthless criminal and Villain Protagonist Porter returns to get revenge on his racist, sadistic, woman beating ex-partner Val, and get back the money that Porter stole from some other gangsters. Along the way the conflict between the two winds up involving Dirty Cops, the Chinese gangsters Porter and Val stole the money from in the first place, The Syndicate Val has since become a part of, low end drug dealers and a High-Class Call Girl. The call girl is the closest thing to a good person, and even she is willing to leave an innocent mark in a Sealed Room in the Middle of Nowhere.
Ilsa: She Wolf of the SS: Most of the movie is typically good versus evil until the very end where Ilsa is killed by a fellow Nazi.
District 9 briefly has the variant where both sides in the struggle over the fate of the Prawns -both MNU and the Nigerian gangs- are utterly unsympathetic and you really hope they wipe each other out.
In the Loop pits Linton Barwick against Malcolm Tucker. Linton is so utterly loathsome and charmless that viewers find themselves rooting for the evil-but-charming Malcolm, even when this means willing him to help start an illegal war. The bastards.
Paths of Glory (1957) by Stanley Kubrick. Admittedly, the bulk of the film is more of a courtroom drama with Kirk Douglas as an idealist officer/lawyer being the obvious good guy, but its World War I setting and overall anti-war message could classify it as Evil Versus Evil when it comes to the two sides fighting a pointless war, with the French generals coming off as arrogant and foppish with little (if any) regard for the life of their soldiers. One could imagine their British allies, or their German opponents, being exactly the same.
In Red State the evil church is killing gays and promiscuous teens out of religious mania. Then the ATF shows up, decides they are all terrorists and decides to murder every single parishioner, including the children.
Invoked and discussed by Augustus Gibbons in xXx by way of explaining his reasoning for recruiting criminals, although it's actually more Black and Gray Morality in that the proper villains are far more evil than Xander, who's more of a low-level underground figure who never sets out to hurt anyone. The only crime we see him commit onscreen is stealing and crashing the car of a zealous Moral Guardianpolitican.
Gibbons: Do we drop another mouse into the snake pit, or do we send our own snake and let him crawl in?
Bully is about a group of vapid, selfish, amoral wastes of space who conspire to commit murder. The victim is an asshole himself, but the film argues that he's only the same key played louder.
Pirates of the Caribbean revolves around this. At least one of the factions consists of amoral pirates. The others include an amoral/somewhat sadistic Psychopomp and the leader of the East India Trading Company (plus the British Navy, which doesn't do much.)
The Alien vs. Predator crossover franchise is an example of this without question. Whoever wins, we lose. The first film shows the last predator teaming up with the humans — only because it was the only way he could win. He died in the end, as well as the other predators who knew of the alliance - though the comrades, on the Immediate Sequel. This is actually a bit of a subversion as neither the Xenomorphs or the Predators are truly evil, as Predators operate on Blue and Orange Morality based around hunting and honor, while the Xenomorphs are just animals following their instincts. In the Aliens' case though their capacity for moral action is called into question since it's repeatedly shown that they're clearly capable of intelligent thought. Maybe they also operate on Blue and Orange Morality. But both are villains to the viewpoint characters, humans.
In Starship Troopers, a federation of warmongering fascists is pitted against a merciless race of alien killers. The first movie was playing sly with the notion that it was humanity that provoked the bugs. The later films however depicted the bugs as being pretty horrible while showing that humanity was still the propaganda-heavy, war-glorifying nutcases they were in the first movie (though with a few more sympathetic characters whereas the bugs are all monsters.)
Frank and Morton in Once Upon a Time in the West. Initially Frank's just Morton's hired gun, but Frank starts thinking about settling down as a businessman - viewing Morton as more obstacle than mentor. The two spend most of the film one-upping each other, with Frank having his men "keep an eye" on Morton and then kicking him off his crutches. It culminates in Morton paying off Frank's men to kill him.
Admiral Marcus and Section 31 vs Khan Noonien Singh, with the Enterprise crew caught in the crossfire.
Harrison vs. the Klingons, again with the Enterprise crew caught in the middle.
The Hangover Part III is centered around mobster Marshall using the Wolf Pack to get his revenge on the Sissy Villain Chow for stealing a lot of gold from him years before. At a certain point it even hits him back: Chow tells the guys a certain Mexican house has the stolen gold Marshall wants back... and it's actually Marshall's house, Chow only used them to get the half he didn't take before.
Crank and its sequel, High Voltage. Chev Chelios is a murdering, drug using, amoral scumbag psycho. The guys who give him what he has coming however are even worse than him.
Pink Flamingos is about two rivals competing on who is "the filthiest person alive". And both indulge in kidnapping, murder, etc.
Swordfish: While the main plot of the film itself averts this, the purpose of the Black Cell is to fight terrorism using methods far worse than those employed by the terrorists.
Gabriel: Terrorist states, Stanley. Someone must bring their war to them. They bomb a church, we bomb 10. They hijack a plane, we take out an airport. They execute American tourist, we tactically nuke an entire city. Our job is to make terrorism so horrific that is becomes unthinkable to attack Americans.
Angel Heart: Private eye Harold Angel finds himself stuck in the middle of a decade-long conflict between Johnny Favourite, a murderous occultist leader who sold his soul to the devil for power, and the Prince of Darkness himself, who feels cheated out of his contract and wants revenge on Favourite.
The theme of "evil against evil" is prevalent in the book The Exorcist, starting with Merrin's archaeological trip to Iranq where he finds a demon statue that the natives stated was an evil artifact to combat evil. This foreshadows Karras' "evil act" of accepting Pazuzu into himself, to save Regan.
Shown Their Work : the demon's Pazuzu, Mesopotamian King of Wind Spirits, monster and main antagonist of the story. As Summon Bigger Fish noted, he was summoned (mainly by pregnant mothers) to combat his arch-enemy and wife, Lamashtu, who was known for killing or kidnapping young children.
In Animorphs, Visser Three and Visser One are usually at each other's throats—Visser Three wants Visser One's spot and she knows it. The Animorphs and Visser One are willing to work together to stymie Visser Three, but they are in a tight position since she can be quite dangerous herself (especially after she figures out at least some of them are human). In one book, the Animorphs, Visser One, and Visser Three all had their own plans to kill off the other two.
In The First Law, The Reveal that Bayaz is every bit as bad as Khalul claims he is; a Manipulative Bastard and psychopathic egomaniac who has used or betrayed or murdered nearly everyone he has ever known for centuries and is responsible for nearly every major war the Union has ever fought, because the Union was secretly founded by him to give him the resources to battle Khalul, who wanted to bring Bayaz to justice for his crimes. Its telling that Khalul by the time of the story is a cannibalisticKnight Templar and Sorcerous Overlord whose own empire, the Gurkish, is built on war, slavery and death after He Who Fights Monsters hit him in a big way, yet Bayaz might still be worse than he is. The protagonists that Bayaz uses all push this trope themselves in various ways, being extremely dark antiheroes at best, but Bayaz is an utter bastard and, worst of all, he is perhaps the only character who wins in the end.
Harry Turtledove has an interesting example in his Worldwar series: we have a lot of scenes of powers often thought of as "evil" such as the Nazis, the Imperial Japanese, and the Soviets fighting the invading Race. The twist is that the Race are much more "civilised" even than the Western Allies (they're possibly an allegory for the Western world in the Nineties) yet they see us as inferior and want to conquer and assimilate us and erase our culture. It can often be an uncomfortable crux for the reader to decide who is the more evil.
It got worse in the sequels (Colonization). When the Colonization fleet arrives and starts unloading civilians, someone uses a nuke against them, killing millions. It was the United States that did it, and to prevent another war from breaking out the President allows the Race to nuke Indianapolis.
Everyone in H.I.V.E. is evil to some degree. Even the leader of G.L.O.V.E.'s rival group, H.O.P.E., hires assassins to kill the world's greatest assassin and a teenaged boy, who just happens to have a "binary brain". It doesn't help that the series is based around an Academy of Evil.
The Lord of the Rings is often presented as a simplistic Good vs Evil, but in fact the conflict between Saruman and Sauron forms an important part of the plot of The Two Towers, although nothing much in the way of real Evil-Versus-Evil warfare ever comes of it. Likewise Ungoliant and Morgoth in The Silmarillion.
The videogame / comic / novel Shadows of the Empire had the Emperor keep Darth Vader and Prince Xizor, head of the criminal enterprise Black Sun, at his right and left hands. Naturally they hated each other; for Xizor it was personal. But they had to remain outwardly civil with each other until the end. It's implied that the Emperor set things up like this because he found it entertaining.
And because it distracts his minions from plotting against him; a man who rose to ultimate power by treachery naturally takes many precautions to avoid falling victim to more of the same.
Unfortunately, this policy led to a complete fragmenting of the Empire upon his death with warlords running rampant.
Also in the Star Wars Expanded Universe it is heavily implied that one of the reasons the Empire was created was to defend the galaxy against extragalactic threats like the Yuuzhan Vong - though less for the sake of the galaxy, and more because Palpatine wanted it. This is unambiguously one of Grand Admiral Thrawn's key motivations.
In Galaxy of Fear, the Big Bad of the first six books is under the employ of the Empire but hates to have Vader coming by and saying pointed things about his budget and how he can't handle meddling children. So Borborygmus Gog starts looking up ways to counter a powerful, violent Force-Sensitive. Vader finds out about it and is not happy.
Hannibal by Thomas Harris. On one hand you've got Dr. Hannibal Lecter himself, serial killer and cannibal, versus Mason Verger who abused his own sister as a child, moved on to molest more children and planned on feeding Dr. Lecter to some pigs he's had trained to eat human flesh.
Harry Flashman is a loathsome, profiteering, traitorous cowardly braggart who'll Kick the Dog for fun, betray his country at the drop of a hat, and lie shamelessly about it all to look like a hero afterwards. But he's generally up against some of the nastiest pieces of work the 19th century has to offer, so you'll (almost) forgive him for it as long as they lose in the end.
Carrion Comfort, by Dan Simmons. While there are good guys and they are the point of view about a third to half the time, the plot is ultimately driven by the two big bad chessmasters. Most of the cast happen to be their pieces, and a good chunk of the cast are sociopathic mind vampires.
Michael Marano's Dawn Song, in which there is a battle for dominion over humanity between the demon lord Belial and his succubus minion who represent the aesthetic side of evil and the demon Leviathan who represents mindless, chaotic ugly evil.
The ending of the Dragonlance Chronicles trilogy has Raistlin, by this point an evil black-robe, helping Tanis kill Ariakas for his own purposes. In the sequel Legends trilogy, it is revealed that Raistlin's ultimate agenda is to kill and replace Takhisis, the head evil goddess of the setting. In the Lost Chronicles trilogy, particularly Dragons of the Highlord Skies, it is revealed that there was in general a tremendous amount of infighting and back-stabbing among the Dragonarmies.
The Dragonlance series does this a lot. The Knights of Takhisis were instrumental in the defeat of the Chaos armies. Lord Soth and several of the Dragon Overlords were killed by more powerful villains after tearing through the greatest heroes on the continent for years. Nuitari, god of the black moon, makes a habit of subtly disrupting any plots by his fellow evil deities that might disrupt the balance of the world. One of the central concepts of the setting is that Evil is typically more powerful, and almost always has the advantage of being the aggressor in a given conflict, but will inevitably turn upon itself and give Good a chance to restore the balance.
This is how the Muggles of The Wheel of Time think about The Dragon fighting The Dark One in the back story, since The Dark One is an Expy of the devil, but The Dragon went on to destroy most of the world - people say "The Dragon Brings Both Despair and Hope" for a reason. This makes people understandably nervous about the coming of The Dragon Reborn, but it eventually turns out that The Dragon was a good guy who got a heavy dose of Mind Rape (which only partly carries over to his re-incarnation).
A better example from The Wheel of Time would probably be the dead city of Shadar Logoth and Mashadar, the amorphous cloud of evil that lives there. Mashadar hates the Dark One and all its minions. However, it's unquestionably a thing of evil that will eat the good guys as quickly as the bad. This is explicitly showcased with the character of Padan Fain, who is imperfectly possessed by Mordeth, the guy who created Mashadar. Fain is unwaveringly opposed to the Dark One. He's also probably one of the three most evil people in the whole series.
Several books also detail the conflicts between the Dark One's various minions. The Forsaken are all plotting against each other and at least a few times have succeeded in stabbing each other in the back. The first book also details a trip through the Blight where the characters are running from worms. They are assured that if they can make it to the mountains, the worms will stop: "The worms are afraid of what lives in the mountains."
In Warrior Cats we have Tigerstar Vs. Scourge during The Darkest Hour. And, depending on your view of them, Stick Vs. Dodge in SkyClan's Destiny may count.
Much of Glen Cook's Annals of the Black Company is devoted to the internal conflicts between powerful evil sorcerers. Much of the original trilogy involves the Lady's struggle to keep her Eviler than Thou husband, the Dominator, from freeing himself, so she can keep ruling her own empire as she pleases.
Happens in-universe in Harry Potter and the Chamber of Secrets, although it's more a case of Jerk Ass vs. Annoying. When Snape and Lockhart are dueling, Harry and Ron think the best outcome would be if they finished each other off. Also, when Harry was revealed to be a Parseltongue and everyone believed him to be dark because of this, somebody theorized he only defeated Voldemort to have no competition.
Caine seems to be bumping heads more with villains like Drake and Penny than he does the heroes in Gone. He actually ends up being the one to kill Penny, and he gives his body to Little Pete for a Mutual Kill with Gaia.
The third book of The Hunger Games gives us two President Evils battling for control of Panem: President Snow and President Coin. They both die in the end.
This is an explicit theme of the Coldfire Trilogy. Gerald Tarrant, one of the two main characters, is an emotion vampire, an Evil Sorcerer, and all around Villain Protagonist. The other main character is Damien Vryce, a warrior priest of the One God, who spends most of his time making sure Tarrant stays pointed at the real bad guys, Calesta and the Undying Prince. This is explicitly a philosophy of the church that Damien follows and Tarrant, during his mortal existence, helped found: if you bind evil to defeat a greater evil, you can change its nature and make it into something better.
Primordium has a complicated example. In it, the Forerunners are revealed to have been at war with themselves (in isolated areas) for many years, with the war now in full force all across the empire. To the main characters, all human, this is an example of the trope, as the Forerunners have treated their species as animals and test-subjects for the Flood for years. Especially evident when the "spirit" of the Lord of Admirals, who fought and lost to the Forerunners once and displays extreme Revenge Before Reason tendencies toward them, finds a ruined city destroyed years ago in a battle. At first he is so overjoyed he is able to control his host and wander the ruins, but is quickly overtaken by sorrow at its pitiful attempts to rebuild itself, musing that humans and Forerunners are Not So Different.
In the first book of the Provost's Dog trilogy, the serial extortionist/childkiller called the "Shadow Snake" targets Amon "Crookshank" Lofts, a vile slumlord who is responsible for the book's other serial murder case. The Dogs take their time investigating, since some of them have family members whose lives were ruined by Crookshank.
In Juliette, or the Prosperities of Vice, the Marquis de Sade tries to portray evil as triumphant, with his decadent villain-protagonists swimming in wealth and power, as they kill, rape, steal, and screw their way through the story. For the most part "wolves can lie down with wolves." Until they can't. Noirceauil murders Saint-Fond for his wealth, and the title character robs several other villains...killing one and leaving another alive because he is so awfully bad (but even that is not convincing; her extreme selfishness would normally lead her to cut his throat just to ensure he would not come back for revenge).
24: Does this A LOT; probably because most evil plots involve groups of bad guys working together (a bit of Truth in Television). But since they're bad guys, they'll turn on each other in a heartbeat.
The Beast and its master were enemies of the five members of the Ra-Tet, at least two of whom were evil.
One of those two, who appeared in the form of a little girl, took action against Sahjahn to stop him from butchering every living thing he encountered.
For that matter, the Beast arc actually has its own Evil vs. Evil arc with Angelus directly working against the Beast (eventually killing him) and its master, at least up until said master actually blackmails Angelus with the threat of permanently restoring his soul to him so that he'll never resurface from Angel's personality again.
Season 8 had this Once per Episode with The Master and whatever monster he had allied himself with. Some larger-scale examples include: the Sontaran-Rutan war, the Dalek-Movellan war, the Dalek civil war, and the Dalek-Cyberman battle (such as it was).
And now, it appears that the war between the Time-Lords and Daleks became this.
The war between the Kaleds and the Thals started out as Black and Gray Morality or even Black and White Morality, but by the time of the classic Genesis of the Daleks, it had become very close to being Evil Versus Evil: the Daleks and Thals are both prepared to commit outright genocide against the others (which the Thals actually do, although their genocide is not complete), and the Thals (who up until that episode had been presented rather sympathetically) utilise slave labour and do not care in the slightest about the mortality rate of their slaves. Despite that, the Kaleds and Thals are both presented as generally less evil than the Daleks and Davros, and in a clear case of Even Evil Has Standards, plenty of Kaleds are appalled by Davros' genetic manipulation of the Daleks into Omnicidal Maniacs. Indeed, more Kaleds are presented sympathetically in this episode than unsympathetically, despite the fact that the episode doesn't scrimp on the not-very-subtle Nazi allegory and makes it plain that Kaled society at large is monstrous.note (While the Thals' more monstrous portrayal in this episode might seem to be a case of He Who Fights Monsters or Took a Level in Jerkass, this episode was set before any other portrayal of the Thals, so this would mean that chronologically, this would be an inversion of Took a Level in Jerkass. On the other hand, the war is described as having gone on for hundreds of years, so it is quite possible that neither the Thals nor the Daleks were anywhere near so monstrous at the start of the war). It's revealed in the first Dalek story from the Thals themselves that there weren't "good guys" during the original war, have changed in the years since, and aren't proud of their history. They wonder if the Daleks, whom they haven't seen in a while, have un-taken their level in Jerkass. (They haven't, of course.)
In the Doctor Who Comic Deathworld, the Ice Warriors and Cybermen battle over the planet Yama-10.
In Black Legacy the Cybermen fight against the Apocalypse Device, which was so terrible it wiped out its Creators, the Deathsmiths of Goth. Finally Cyberleader Maxel self-destructs his ship to prevent it escaping its world.
Downton Abbey: Sarah O'Brien and Thomas Barrow were best friends who used to join up to play cruel tricks on others, including trying to frame Bates for theft and in O'Brien's case the far more serious 'trick' of causing a miscarriage for one of the other characters. By series three, because Barrow was unkind to her nephew, Alfred, O'Brien and Barrow became enemies and turned their tricks on each other.
Farscape has Scarrans vs. Peacekeepers. Both sides want to take over the galaxy and kill everyone who disagrees with them. Scorpius tries to convince John that the Scarrans are worse, but, given that the Peacekeepers have been hunting him down for a few years, it rings hollow.
Heroes: Gives us the conflict between insane serial killer Sylar and ruthless Knight Templar organisation the Company.
In most Kamen Rider shows, especially those in the modern era, present these sorts of conflicts. Sometimes, it's one monster fighting another monster, such as The Greeed at most times when it comes to stealing Core Medals from each other. Other times, it's a villainous Rider taking on an equally villainous monster, like with Kamen Rider Eternal vs. the Eyes Dopant.
LOST: Has the conflict between Ben Linus and Charles Widmore in seasons 4 and 5, as they vie for control of the island. In season 6, it seems to be setting the stage for another one in addition: Charles Widmore versus the show's real Big Bad, The Man In Black. By the end of the series, Ben gets redeemed. And Charles seemed to be on that track, but then Ben killed him... His full redemption doesn't come until after that.
Masters Of Horror: The episode "Pick Me Up" has Wheeler, a serial killer truck driver, V.S. Walker, a serial killer hitchhiker. The eventual winner? The serial killing ambulance driver duo who pick them up at episode end.
By the end of the first season Regina (the Evil Queen) and Mr. Gold (Rumpelstiltskin) have all but declared war on each other. It really starts when Regina uses the theft of Gold's Tragic Keepsake to force him to admit that he remembers who he really is, then team up to frame Mary Margaret (Snow White) for murder, only for Regina to realize too late that Gold manipulated the whole thing so that by the end it was obvious that Mary was framed and all of the evidence pointed at Regina.
This feud continues into the second season, although they brief team up to stop a greater threat, only for Regina to end up joining said threat, and when Gold screws her over with that, she finds a way to hurt him back. Additionally, Captain Hook's whole motivation on the show is too destroy Gold for Revenge, and then Tamara and Greg enter the picture to go against Regina, with their clash being described in actual TV promos as "Evil Versus Evil".
When the third season brings the Wicked Witch of the West in gunning for Regina, the promos hype it as "Wicked Versus Evil." Less prevalent in-series, as Regina's Heel-Face Turn has really started to take hold, and is what enables her to defeat the Witch in "Kansas."
Mesogog: Looks like this planet has one too many evil villains, and I have no intention of leaving.
Power Rangers Operation Overdrive: This trope is a major part. The Corona Aurora, an object of god-like power, is so sought after that there are a total of four distinct villain factions fighting the Rangers and one another for it; they occasionally get along, but most of the time, they're fighting one another as often as they fight the Rangers. Even after being shown they're a much greater threat working together, they go right back to trying to kill each other afterwards.
Power Rangers Super Megaforce: Professor Cog lures the Megaforce Rangers to Corinth so he and his Grinders can invade Earth unimpeded, but Prince Vekar refuses to be one-upped, so he and the rest of the Armada come to Earth to battle Cog while the Rangers are occupied.
Revolution: The minute Sebastian "Bass" Monroe and Randall Flynn teamed up at the end of episode 11, savvy viewers knew that they would have to turn on each other at some point. Bass is a former marine who rules the Monroe Republic as a dictator, and has a lot of loyal (or cowed) men and weapons at his command. Randall, in contrast, is a former bureaucrat who dresses up sharply, relies on slasher smiles and bargaining, is a non-combatant who mostly operates solo (he had one goon named Mr. Austin, but the guy backstabbed him and got killed off in episode 16), must rely on electrical toys to take down people, and has to rely on Monroe's men to protect him when he goes out into the field. Sure enough, episode 18 has Bass confront Randall about holding out on him about the Tower and orders him killed. Randall is easily defeated in this brief confrontation, but he survived by offering to take Monroe to the Tower himself and had to get reduced to a mere toady to stay alive.
Spartacus: Blood and Sand: The villains may all be against Spartacus and his allies, but that doesn't mean they have any true loyalty towards one another. They're all perfectly happy to backstab and murder one another to succeed. Then a much darker example occurs in War of The Damned where some Romans are portrayed as decent people caught up in a war, and some of the rebels are basically psychotic murderers. It's sort of a combination of Grey and Gray Morality and this trope.
We have the tyrannical Goa'uld fighting each other over territory and other things and have the Replicators (except for the later human-form replicators they're not evil per se, but a threat to all life) fighting everyone, including the Goa'uld.
The Trust is a shadowy group of Earth businessmen who try to assassinate Senator Kinsey in season 6, then briefly take the Earth/Goa'uld war into their own hands in season 8.
The Asurans battled the Wraith, erasing human life to deplete the Wraith's "food sources". In the end the Asurans proved to by far the greater threat, leading to an alliance between the humans and a Wraith faction to eliminate them.
The Wraith are no more friendly amongst themselves than the Goa'uld — that alliance contains nine factions, not the three you'd assume at first glance.
There's a less direct example in the episode "Critical Mass". The Trust, having been taken over by the Goa'uld, plans to blow up Atlantis in order to prevent the Wraith from gaining access to the city, making their way to the Milky Way and gaining a foothold in our galaxy. The fact that it would have dealt a significant blow to Earth was just the icing on the cake. With the SGC, the Tok'ra, the Free Jaffa Nation, the Ori and the Lucian Alliance to contend with, the last thing that the few remaining Goa'uld needed was another enemy to fight. Unfortunately, we never got to see a proper encounter between the Goa'uld and the Wraith.
The Enterprise story "In a Mirror, Darkly" is also an example of this trope- the being set entirely in the mirror universe, there are no good guys, and the protagonists delight in backstabbing one another at the least possible opportunity as well as fighting the Tholians.
The standard operating environment. Sam and Dean, who frequently drift into being anti-heroes in their own right, are surrounded by major league evil - and often find themselves stuck working with it against something even worse. You know that things are bad when Heaven is run by jerks and God is off on sabbatical somewhere, leaving you to deal with angels and demons that are often kind of hard to tell apart.
The demon Crowley is an amusing example of this. He manipulates and double-crosses everybody in sight, from the protagonists to his own demonic peers, in order to save his own neck, his comfortable job as a soul merchant and (incidental to those goals) the world. Though a useful ally and unusually honest for a demon, he never makes any attempt to pretend he isn't evil. This makes it all the more impressive that he convinces the good guys to keep working with him even after they've been tricked, thrown under the bus, beaten half-senseless and otherwise abused as a result of listening to him.
Crowley becomes the instigator of this again in Season 6; it's eventually revealed that The Mother of All came to Earth and started building armies of monsters in response to Crowley's plans to steal all the souls from Purgatory - the Mother's domain. And when the Mother's killed, the last few episodes of the season are still spent dealing with this trope, as the Winchesters find themselves stuck in the middle of the power struggle between the remaining contenders for the position ofBig Bad: Crowley, Raphael, and Castiel, who has jumped off the slippery slope to prevent Raphael from turning the planet into a graveyard by restarting the Apocalypse. In the end Castiel decides to cut Crowley out of the deal, in response to which Crowley teams up with Raphael, but Castiel Out Gambits them both. He kills Raphael, ascents to godhood, and makes Crowley his servant not much later. In season 7 he's killed due to the strain of containing inside himself, in addition to millions of souls, the Leviathans - absolutely ancient creatures from Purgatory who wish only to consume. Which leads to...
Crowley instigating this again in season 7. He attempts a Villain Team-Up with the Leviathans' nominal leader, but is brusquely rejected. Then he orders his demonic forces to ignore the Winchesters so they can hunt Leviathans around the clock.
Though less common than Face vs. Face, and FAR less common than Face vs. Heel, sometimes happens in pro wrestling, particularly when Vince Russo is at the helm. Making one a success can be difficult though, since one of the cardinal rules of any match is that the audience should be rooting for someone. That said, it can work if the match is a prelude for one of the Heels to turn Face.
One major example would be The Corporation vs. The Ministry feud, where both sides were portrayed as bad guys. Though in the end those two groups would merge together to form the Corporate Ministry, and it was revealed Vince McMahon was the mastermind behind both stables all along. It still works as not every member was in on the plan, though those members left prior to the merger and turned face. Though even in the Corporate Ministry there was fighting within the group, especially between The Undertaker and Triple H.
Very common with Shawn Michaels whenever he was a heel. In addition to feuding with both mostly-heel Hart Foundation and theoretical heel Stone Cold Steve Austin, Shawn also feuded with heel Rick Martel over the affections of Sensational Sherri. Beyond that, he was involved in a three-way feud with Chris Jericho and Batista in 2008, where of the three only Batista was really a face (Shawn eventually turned face after Batista left the feud and Jericho beat up his wife).
Happened a weird way a couple of times when Shawn, mostly a face, would be allied with another face (John Cena, Chris Benoit, Goldberg, Austin) against a common (heel) foe, but with everyone involved painfully aware of Shawn's eventual inevitable betrayal… which, sure enough, always came. Almost always via Superkick.
He also spoofed the trope when forced to defend his European Title against then-ally Triple H, overdramatizing the buildup, throwing the match, and then cutting a tearful promo about the loss.
Any Triple H vs. Kurt Angle match from 2000-2002 was this essentially. Triple H was the sledgehammer-wielding Villain Sue against the pompous Smug Snake Kurt Angle who wanted to take the guy's wife. Though they were both heels, they were tenuous allies at best and vicious enemies at worst. They would feud on and off from year to year, with neither really turning face at all (the closest being their No Way Out match where Triple H was running off of Determinator face heat). During this period Triple H even paused during his catchphrase to allow the audience to finish it — a way of hinting to the smart marks that he was going to turn face. He didn't.
Undertaker vs Big Bossman in a Hell In A Cell match was this. This one wasn't so successful, mostly because they had no real chemistry or feud, so the crowd had nobody to root for.
Shawn Michaels vs. Bret Hart at Survivor Series 97 is the most infamous example. While Bret had the crowd behind him because it was Canada he was still in storyline a Heel. It's interesting considering it was Face vs. Face last time.
During the "Kayfabe" era, the only time villains typically fought were in battle royals. However, there were at least two "heel vs. heel" matches in the WWF, both in 1986, and one in NWA two years later:
Randy Savage vs. Jake Roberts on an episode of Saturday Night's Main Event (a match that bore no resemblance to their matches five years later, where Savage was the face and Roberts the worse-than-evil heel. Both were heavily booed and neither showed much respect for the other. In fact, somewhat foreshadowing Roberts' behavior toward Miss Elizabeth during the 1991 feud, he once tried to counter Savage's then tactic of pulling Elizabeth in front of him to shield off an attack by pulling Damien from his bag and nearly throwing it on Elizabeth!
The WWF was indirectly responsible for the 1988 heel vs heel match as well. When Arn Anderson and Tully Blanchard signed with Vince, they were World Tag Champions. NWA was not going to let the belts go with them. Due to their status in The Four Horsemen the only team with as much heat as Tully & Arn was Jim Cornette's Midnight Express. The fans cheered for Beautiful Bobby and Sweet Stan, who became the first team to simultaneously hold the US and World belts.
Face and Heel aside, the various feuds and matches between The Undertaker and Kane can count as this. Both wrestlers, even when portraying Faces, maintain a gimmick of being pure evil. At best, they can be in the Noble Demon category. This means that any match between them is literal evil vs evil.
The two biggest stables in earlier 2014 The Shield and The Wyatt Family are both heels, and after several teases, have wrestled at Elimination Chamber. Throughout the feud, both teams were heavily cheered by the fans, due to them all being interesting and well-developed characters.
Comedian Juston McKinney mused about a hypothetical ride between a Serial Killer picking up a rapist. Both keep trying to psych each other out over who should be the victim then Gilligan Cut to a police station where one of them files a report.
The biggest two examples being the Eldar and the Tau. The Eldar are psychic space elves that can see the future. They fight against Chaos, which is what Eldritch Abominations fear when they're up late at night. The fanbase tended towards them being the good guys, so the latest editions of the game has played up the "Manipulative Bastard" part to 11 and making it clear that they're all about the long game. In one example, they caused an Ork warlord to attack the Human world of Armageddon, killing billions in order to save a few thousand Eldar lives; in another, they happily attacked both Orkish and Imperium worlds in order to deny the Tyranids biomass. Further, an Eldar captured by the Imperial Guard makes it perfectly clear that once they are back on top they will systematically kill every single human, or Mon-Keigh, in existence.
The Tau are anime-influenced space-communists that fight for The Greater Good, and are the closest thing the setting has to a neutral or even good faction. That is, if you ignore the fact that their entire race is being mind controlled by their leaders. Not wanting such an obvious good race in the series, Games-Workshop pointed out that the Tau's plans for humanity include forced sterility, slave camps, and genocide. The kicker? They're still the only thing close to a good race the game has.
The Imperium gets this too. For every hardworking adept who agonizes over every difficult decision, honorable space marine, or working class guardsmen with balls of steel they show you; they are contractually obligated to show ten Knight Templar inquisitors screaming "EXTERMINATUS!"
Likewise, the fundamental premise in Warhammer Fantasy. Its nice guys - High Elves, Wood Elves, Bretonnians, Empire, Dwarfs - are not.
This is sort of built into the alignment system in Dungeons & Dragons, though it's more a result of any Evil alignment taking on Order Versus Chaos: chaotic evil and lawful evil characters theoretically hate each other as much as, say, good and evil ones, and while this isn't applied so much to mortals, the war between demons and devils, which is known as the Blood War, is mentioned more often than the war between celestials and fiends. It was a major element of the 2e setting Planescape.
The Third Edition Dungeon Master's Guide says "...evil rarely gets along with evil, for the desires of one selfish and destructive being, by definition, conflict with the desires of other selfish and destructive beings.
The two Fiendish Codexes explain that there is an infinite number of demons, and there's more of them spawning at all times. Angels, Archons, Devils & company are in a finite number. The Devils exist in fact so they can use their superior tactics and team work (due to their Lawfulness) along with similar weapons as those used by the demons, to keep the demons in check. The books make it explicit that if the Devils weren't around, the demons would swarm and destroy all of creation. The books also hint that if the demons vanished, the Devils could probably conquer the Multiverse, being a race composed entirely of Magnificent Bastards and Chessmasters. And in the 2nd Edition of the game, the various forces of good took time to fan the flames, hoping to break their enemies against each other. In the Planescape boxed set "Hellbound: the Blood War", there's even an adventure where player characters discover high-ranking angelic beings funneling weapons and armor to their favored side in the war so more and more of the fiends would be killed. Some demon sub-races are also enemies of other demon sub-races (bebiliths eat other demons, for example). Some members of the higher ranking devil sub-races get promoted to the next higher-ranking sub-race by getting their direct superior killed or demoted, while some pit fiends (the highest-ranking sub-race) do the same to replace the devil dukes and duchesses who themselves are The Starscream to the archdevils. There's also much enmity between the archdevils (Dispater and Mephistipholes vs. Baalzebul, Prince Levistus vs. Princess Glasya, all the other archdevils trying to take Asmodeous' throne) and the demon lords (Juiblex vs. Zugtmoy, Baphomet vs. Yenoghu, the three-way battle between Graz'zt, Orcus and Demogorgan). In the Complete Scoundrel supplement, a prestage class called the Malconvoker is introduced which follows the teachings of a book called Vital Pact to impersonate evil for the sole purpose of summoning fiends to fight other evils and other with perpetuate all of the fighting between evil above, since the Celestial beings are too few to win their war against evil otherwise.
4th Edition has several instances, the most notable being the god of war Bane and his eternal war versus god of destruction Gruumsh. While Bane revels in conquest and power, one of his prime commandments is to ALWAYS obey the rules of war. He also likes his followers to be rigidly disciplined and wants to preserve the world so that it will be worth conquering. Gruumsh on the other hand revels in utter destruction and encourages savagery in his followers. Both want to be the uncontested god of war, and thus they've been fighting for eons over their differences.
4th Edition retained the Blood War, but in heavily modified form. Firstly, its importance has been de-emphasized, citing its Plot Tumor-esque nature and the way it made Good and Neutral alike seem pointless and impotent. Secondly, the underlying motives have been changed from the lofty, philosophical abstracts to something much simpler: Asmodeus stole a shard of the literal Heart of the Abyss to create his infamous Ruby Wand, before he murdered his divine master. Asmodeus wants the rest of the Heart, figuring it would make him even more powerful. The other Arch-Devils want the Heart for themselves, figuring it would make them powerful enough to dethrone Asmodeus and conquer The Multiverse in his place. The Demons want the Heart's shard back. Like all of 4th edition, this change has been controversial.
An orc tribe's worst enemy tends to not be a human kingdom, a clan of dwarves or even a Hidden Elf Village, but a rival orc tribe, and the same applies to hobgoblins and their tribes. Only a sufficiently powerful Big Bad can terrify rival tribes into working together, and the result tends to be a Keystone Army. If the Big Bad dies, rival orc and hobgoblin tribes who were previously intimidated into cooperating will turn on each other with a vengeance.
The Chromatic Dragons (black, blue, green, red, and white), are all evil (blue and green are Lawful Evil, black red and white are Chaotic Evil), and all obsessed with gathering hoards, gaining territory, building power, and destroying anything good (especially the good Metallic Dragons). However, they have no love for each other either, and they will fight to kill or chase each other away (even if two dragons, a black and a green for instance, manage to form a truce, eventually and inevitably one or the other will break the truce and resume hostilities). The worst are red dragons, the archetypal evil dragons, who will slaughter anyone and anything in their pursuit of their desires.
Frost giants (Often Chaotic Evil according to the Third Edition Monster Manual) often kill white dragons for food and armour or capture them to use as guards. There are both many evil and many non-evil githzerai, but both attack the githyanki and mind flayers on sight. Meanwhile, githyanki and mind flayers are both evil and attack each other on sight as well.
Salamanders hate efreet.
Each beholder believes its appearance to be the ideal of the beholder form. As such, all other beholders are inferior at best, and ones that differentiate too much must be destroyed.
Though both races are Chaotic Evil, there's no love lost between the Qlippoth and the Demons; the former used to rule the Abyss before the Demons stole their place, and they fight ceaselessly to take it back or to hold it, respectively.
Any two Ravenloft darklords whose domains share a border are quite likely to be bitter enemies, and most domains have one or more lesser villains waiting in the wings to seize power if the dominant evil should slip up. The most famous of rivals, Strahd and Azalin, have been feuding and sabotaging each other's schemes for centuries, although the nature of the Land of Mists prevents opposing darklords from simply overrunning their rivals' territory.
The post-war Dragonlance setting is like this. With Takhisis banished to the Abyss, her five Dragonarmies turn on each other. Now, the five factions are just as apt to fight each other as they are to attack the good guys.
This is the very principle behind the Tabletop RPGNecessary Evil. An alien invasion has wiped out all the superheroes, so the only ones left to defend the world is the supervillains. After all, you can hardly conquer the world if it's already been destroyed by aliens, right?
The Character Alignment system for Palladium games (such as Rifts) establishes that Aberrant characters (think Lawful Evil) refuse to have anything to do with the other Evil alignments and finds them disgusting. It's quite possible to have an all-Aberrant party run a lot like an all-Principled party with only a few slight differences.
An In-Universe case for Rifts is the Coalition States vs. all D-Bees, once one reads the various sourcebooks and is forced to admit that the vast majority of non-humans on Earth genuinely are as evil and dangerous as the Coalition States portray them.
In the Old World of Darkness, Agents of the Wyrm don't take kindly to someone mixing in traces of the Weaver with their plans. This is likely to cause some mayhem when Pentex figures out the true backing of the head of their Avalon toy company subsidiary.
Savage Worlds: Necessary Evil envisions a world where supervillains are the only powerful humans left after a massive alien invasion. They form a resistance to fight back the occupiers, but aren't necessarily reformed. If they drive back the aliens, they'll be in a position to take over the planet.
An option for In Nomine casts the setting as Dark Low Contrast, where angels and demons are both wicked, violent fanatics and nobody at all is looking out for humanity's interests. The PCs in such a campaign will normally try to be better than the rest, though.
Crops up from time to time in Magic: The Gathering. In the Innistrad cycle, one subplot follows Liliana Vess, whose only goal in the plane is to kill the demon Griselbrand to keep him from collecting on the bargain she made with him long ago. Her pursuit of this agenda ends up saving the entire human population of Innistrad.
Pretty much the point of a game of Paranoia, as the characters, PC and NPC alike, are all backstabbing traitors.
Though it tends towards Grey and Gray Morality on the whole, Eberron has its share of purely malevolent elder evils. That does not mean said elder evils get along. The Lords of Dust are prone to internecine conflict, since different factions of them serve different Overlords who tend to have wildly differing agendas, and they all view the Inspired as a bunch of posers butting in on their turf when they have no right to; the Inspired, for their part, don't like the Lords of Dust because they view them (and especially the threat of them managing to wake one of the Overlords up) as a threat to their plans to create perfect order in the mortal world and thereby anchor their own dimension in its current Lawful Evil state; to top if off, nobody likes the Daelkyr, mostly because even the most powerful demon or Inspired can't predict what thosemaniacs want, and if the Daelkyr have any opinion on the matter (or any particular conflicts among themselves) they're not chatty about it.
The Grand Theft Auto series is one of the most infamous examples of this trope. The Fridge Brilliance is that all the protagonists and antagonists are murderers and criminals trapped in a world of murderers and criminals. Sometimes, the protagonist does things almost as atrocious as the things the antagonist does, and many of them seem to be worse than their enemies. Here, in fact, the white morality no exist.
Tommy Vercetti of Grand Theft Auto: Vice City got the most characterization as a villain. Although he appears to be criminal out of necessity in the beginning, he's not just punching a clock; he's been a lifelong career killer, never wanted to be anything else, and has no Freudian Excuse behind it. He has no standards beneath him and doesn't appear to be any better than any of his enemies, yet still manages to be the most Affably Evil character in the series. Not to mention one of the toughest. Dude takes some serious punishment whenever he ain't dishing it out in cutscenes. There are some very good reasons why he became sort of the 'unofficial face' of the franchise, especially to non-players.
Another good example would be the scene of the Grove Street Families vs. the C.R.A.S.H. from Grand Theft Auto: San Andreas. While the Grove Street Families and Ballas are rival gangs, C.R.A.S.H. is supposedly a group of cops who claim that their approach to work is about "percentages" and they really want to manipulate bands and eliminates. But in reality the group C.R.A.S.H. is corrupt at the core and terrorize gang leaders in much the same way as they would a street gang. Even the very leaders of this group (Tenpenny and Pulaski) are guilty of various crimes.
Eggman: How can I take over the city and begin building the Eggman Empire if there IS no city?!
Notably, one of the stages offers the mission of helping Eggman (to help destroy Black Doom's floating stone battleships) as the HERO mission. The Neutral mission is to ignore both sides, and the Dark mission is to destroy Eggman's fleet and keep the alien ships afloat. Yes, fighting against Eggman in this case is treated as the more evil option.
Syndicate. Set in a future where human life is cheap (and entire populated areas are subject to "lunchtime nuclear testing"), corrupt syndicates vie for control of the world, with no qualms whatsoever about the idea of killing civilians in the process. Or just brainwashing their enemies into doing their bidding if violence is too much of a hassle. In the 2012 remake, this continues, but also throws in the Downzone Subverters, who are Bomb-Throwing Anarchists. One background conversation has someone say that the Subverters haven't done anything for the average Downzoners, whereas the syndicates at least kept things clean.
Gargoyles Quest, a spinoff of Ghosts N Goblins, puts you in the role of Firebrand the Red Arremer, a recurring miniboss from those games and a member of the invading demon army. He takes a break from laying waste to the human world in order to heroically defend Hell from the invading demon hordes of another Hell.
The sequel, Demon's Crest, sees Firebrand escape from gladiatorial combat to hunt down Phalanx, a demon who has stolen several powerful crests from him and is using their power to rule the world. The catch? Firebrand wants the crests so he can rule the world.
Played for Laughs in Overlord. You play as the reincarnation of an Evil Overlord seeking revenge on the heroes who defeated you. Conveniently, all seven of them have become so corrupted in the meantime that they rival you in evilness, are now virtual embodiments of the Seven Deadly Sins and enable you to still become a Villain with Good Publicity while killing them if you play your cards right. In fact, the seventh hero is possessed by the actual Evil Overlord, and is the one that corrupted the others. Surprise! You're not the real Overlord, you're a Tomato in the Mirror. And in the sequel you play as the previous Overlord's son fighting against an oppressive Empire that seeks to eradicate all magical beings (that would include the new Overlord and his minions too). Also, the Big Bad is the power-mad Emperor seeking godhood willing to summon a man-eating Eldritch Abomination to accomplish his goal. Compared to that, the Overlord looks almost heroic! Key word: almost.
Before he got into mini-games, Wario of Super Mario Bros. came up with the idea of stealing money from other bad guys. This has worked out rather well for him. It hasn't stopped other bad guys from stealing money from him.
In Mass Effect 3, Harbinger will send Reaper troops to attack a major Cerberus facility near the end of the game. One of your companions will remark that it's about time they tried to kill each other.
Star Warsswims in this trope — most conspicuously in the video games, Dark Siders fight each other if anything more intensely than they fight anyone else.
In Knights of the Old Republic, taking the Dark Side path means fighting Darth Malak for control of his/your war machine, with the conquest of the Republic covered in the epilogue. Additionally, a Dark Sider in KOTOR 2 will face Darth Nihilus, who draws his power from the same source as the player character. Evil Counterpart to a good character, he becomes Not So Different for an evil one.
Ditto for Jedi Knight, Jedi Academy, and any other game that gives you a Dark Side path...
Also ditto for the films and the Expanded Universe, which has been a very colorful place since Palpatine was overthrown in favor of the New Republic. The New Republic has completely collapsed in favor of some kind of uneasy coalition of monarchical Imperial factions, independent core planets, and alien invaders by this point, and most of the Skywalker family is back on the Dark Side — and this without being a deliberate Crapsack World.)
Star Wars: The Old Republic: Playing a dark side character, regardless of faction, will inevitably and almost by definition result in this trope. As a Republic hero, you can sometimes get a letter (and credits) from a Sith thanking you for taking out the competition after killing (or otherwise defeating) a Force-user.
City of Villains is a good example of why this trope exists. The few truly evil contacts (Westin Phipps in particular) produce a good deal of controversy about whether they're "too evil." Thus, more than half the game's missions could very easily be rewritten for heroes. Many contacts have forced unethical traits and selfish motives written in for why you're stopping a villainous organization from realizing their plans. You spend more time fighting your "patron" organization of Arachnos than you spend fighting Wyvern or Legacy Chain (Longbow are like cockroaches, though…).
Probably the only way Kratos could seem even remotely sympathetic is making the Greek pantheon out to be gigantic bastards, especially Zeus. To be perfectly fair, one glance at mythology will tell you this isn't far off... Most of the Greek Pantheon has few, if any, redeeming qualities aside from the fact that they replaced something that could be considered worse from the Ancient Greek point of view.
The gods of Olympus actually invoke this trope by sending Kratos, a Sociopathic Hero, to battle other monsters that nobody else can defeat. Kratos utterly slaughters each one, then moves on to the next. He even becomes powerful enough to kill Ares, the eponymous God of War, and takes his place.
The creators of the game have stated that the reason they didn't go with a more traditional Greek hero is because they felt that such a character wouldn't last five seconds in the world they were trying to create. There are actually several minor characters in both games who embody various versions of those iconic heroes, and they are usually killed horribly within seconds of their appearance. Perseus lasts the longest, but even he is not immune. Still, if the creators had read the original myths a little more closely, they would have realized that the only thing separating Kratos from those so-called "heroes" is that Kratos doesn't even try to justify his actions by calling them noble. He just kills things. A lot of things.
Some parts of Dungeon Keeper pit you against rival keepers, but these events are mostly incidental; the main focus of the plot is still about fighting heroes.
Far more focus on this in the unofficial expansion pack Ancient Keeper, in which the focus is on proving that you're tough enough, vicious enough, and (above all else) clever enough to take your place among the ancients of your kind. You still fight heroic forces constantly, but crushing other candidates for the title (often on their home turf) and surviving the current ancients' tests is the goal.
Dungeon Keeper 2 gives you an ongoing rival keeper named Nemesis, who commands all of the other rival keepers you face. Again, the primary goal is killing the heroes, though this time it's to take the Portal Gems they guard, some of which have already been looted by the other keepers.
Cortana: You might want to try sitting this one out.
In Halo 3, at one point the Prophet of Truth is about to activate the Halo Array and unleash destruction upon the galaxy. Nobody wants that, not even the parasitic Flood, so for one brief moment you must fight alongside Flood combatants and decimate Truth's bodyguards. Like in the example above, you can even hang back and let the unstoppable hulks do the heavy lifting for you.
Excluding the Protoss campaign, you play as a commander in an evil force throughout StarCraft Brood War. This is even lampshaded by the Queen Bitch of the Universe herself.
Duran: Do you think they suspect anything, my queen? Kerrigan: Of course, Duran. They're simply siding with the evil they know over the evil they don't. They just don't realize exactly what it will cost them.
Several scenes in the Half-Life series feature the human enemies and alien enemies fighting each other. In Half-Life 2 and its Episodes, Combine troops, Antlions, and Headcrabs/Zombies all willingly attack each other. After an epic battle between a mob of Zombies, a swarm of Antlions, and Freeman and his Vortigaunt ally, the Vortigaunt comments on how the Antlions and Zombies continue to fight even after the two had escaped.
GoldenEye: Rogue Agent is a prime example. The only real difference from being Bond is that you can use human shields.
Wizardry sums it up this way: a good man helps an old lady across the street. A neutral man crosses the street and helps an old lady across while he's doing so. An "evil" male PC helps a young lady across the street. Your enemies help an old lady halfway across the street.
Team Fortress 2: Two teams of ruthless, bloodthirsty mercenaries gleefully blasting the shit out of each other, with only the flimsiest justification. They're being led by two identical twins who have hated each other since birth, and are being secretly manipulated by their weapons supplier to provide her a constant source of money. Forever and ever.
Fable will always pit the Hero against the villain Jack of Blades. However, the "Hero" can be evil himself if he so chooses, so his motivation is left up to the player to pick: is he fighting Jack to avenge his loved ones and save the world, or to keep Jack from conquering the world so that he can conquer it himself?
Disciples 2: Dark Prophecy features this near the end of the Legion of the Damned's saga. It turns out that Uther isn't really the reincarnation of the Legion's god, but just some evil brat siphoning his power and slowly killing him. Since you're one of the god's loyal servants, you have to fight him in the end. This has the odd effect of giving demons from hell the surprisingly sympathetic motivation of trying to save their god.
One of the BEST campaign twists in known history. Added bonus? The fight against Demon Uther is quite possibly the toughest boss in the game.
Really, any fight between the Legions of the Damned and the Undead Hordes.
In Prototype, we have the sociopathic, nigh unstoppable monster who eats people. He's the player character, and the closest thing to a hero we have (he very slowly develops something akin to a conscience). Then we have the BlackWatch, a secret military organization who created the viral threat in the first place (to target racial minorities), tested it on civilians, and are planning on nuking Manhattan to stop its spread. Then we have Elizabeth Greene and her viral mutants, who essentially intends to unleash a Zombie Apocalypse because she can. The man-eating dude wins. Yay?
Amusingly it's also shown that The Blacklight Virus, the new Alex Mercer, has far and away more of a conscience than the original ever did. Which pushes him a little further to the grey side at least.
Warcraft likes this trope. We have the demons of the Burning Legion heavily at odds with the Undead Scourge even though the magic they use and their ultimate aim is almost identical (and the Scourge used to be part of the Legion). Being the original "owners" of Azeroth, the Lovecraftian Old Gods are at odds with both the Legion and the Scourge although they are implied to have a degree of influence on both of these factions. Illidan's motley crew of (evil) Blood Elves, demons and Naga are engaged in heavy fighting against the Legion due to Illidan's failure in taking out the Undead Scourge for the Legion.
In addition, The Frozen Throne featured the Plaguelands Civil War, a four-way war within the Scourge between the loyalists of Arthas, the loyalists of the Legion, and the remaining Alliance forces (who are generally good guys but are led by a racist Jerkass Lord Garithos).
The Dark Iron dwarves initially fought in the service of Ragnaros against the Blackrock Orcs, who served the Black Dragonflight. In Cataclysm, however, Ragnaros joins forces with Deathwing.
The main opposition to the gronn-ruled ogres of Outland, which prove a threat to the Alliance and Horde's Outland allies, happens to be the Always Chaotic Evil Black Dragonflight, which is seeking to avenge the deaths of many of its members at the hands of Gruul the Dragonkiller.
In Wrath of the Lich King, the Scourge conquered the Nerubians and almost conquered the Drakkari ice trolls, both of which are quite evil (the ice trolls especially so, even compared to the evil and barbaric majority of the non-playable trolls). In Drak'Tharon Keep, both the living trolls and their allies, and the undead trolls and other Scourge members attack the party as they make their way up the keep.
Mario & Luigi: Bowser's Inside Story pits Bowser up against Fawful, who's taken over the Mushroom Kingdom and booted him out of his own castle. Again. This time, however, the Super Mario brothers, for the most part, play a supporting role in the game, powering up his body when necessary (including making him a giant in order to Megaton Punch castles). Later on after Fawful and the Dark Star go One-Winged Angel it's up to Bowser to save the Mushroom Kingdom.
If you take the evil path in the vast majority of RPGs, you're still going to have to fight the same evil Big Bad. In a BioWare game, your quest will be close to the same regardless of your alignment, including a struggle against the minions of the Big Bad; maybe, at the end, you'll be given an option to join them instead of fighting them; otherwise, you'll just prove to be Eviler than Thou.
In The Godfather, your character Aldo Trapani runs a protection racket for the Corleones, doesn't hesitate to cause property damage or (threaten to) brutalise shopkeepers in his extortion attempts and can kill people in a wide variety of ways. Every copper in NYC is a Dirty Cop who at best never turns down a bribe and at worst is a rapist. The other Families don't have the moral high ground, though, as their members are always itching for a fight, rule their turfs with iron fists and don't shy from shooting up civilians blocking their line of fire to you.
Any enemy in Doom that either has a gun or throws a different type of fireball can cause monster infighting. The "former humans" are most prone to this, as they're the only enemies in the game whose weapons can hurt others of their own kind. The Arch-Viles can be humorous with this, as they can resurrect an enemy who they just killed and then get into another fight with them, and repeat the process.
The Cacodemons and Barons of Hell are also good examples of this. Dead Cacodemon corpses can be found in "Baron halls" and wall images of crucified Barons of Hell can be found in some areas where Cacodemons are the predominant enemies. This feud between the Barons of Hell and Cacodemons is also in the expanded universe Doom books. Cacodemons crucified Barons, despite lacking hands or anything resembling tool-manipulators. That's some serious hate.
Invulnerability code in Doom II. Last level, Icon of Sin. More fun than actual cockfighting, especially when the Arch-Viles and Pain Elementals are spawned. Shame there's no easy in-game way to eliminate corpses, it gets somewhat crashy after a few hours of this carnage.
There's a level in Doom II with a room that only has a Cyberdemon and a Spider Mastermind in it. They're each trapped on little platforms and the whole exercise does little but allow you to pit these two fearsome creatures against one another by coaxing a monster infight between them.
Super Robot Wars has this as a thing that can be done in the game provided there are 2 sets of enemy forces on a battlefield, Primary Enemies (Red) and Neutral/Secondary (Yellow) despite them usually targeting you, they will go for each other if they are in range at times, firing shots and destroying each other, which in larger levels can make life a tad easier. Different villains from various anime are often pitted against each other, with additional original villains throw in.
Modern Warfare 2. General Shepard's Infamous Shadow Company vs. Makarov's Ultranationalists. And you in the middle. How fun! Although it only lasts a mission but it's far easier just to make the fight as even as possible then sit back and watch the carnage (typically shadow is ahead).
BioShock. The idealist objectivist turned bitter despot Andrew Ryan versus the sleazy power-hungry smuggler and rebel Frank Fontaine, both with hordes of insane, vicious mutated Splicers at their command. And you're a mind-controlled test tube baby used by Fontaine (under the guise of Atlas, a noble rebel and family man) to kill Ryan, then he turns on you. He dies. Only you and Tenenbaum, a Jewish Nazi collaborateur and The Atoner, survive the events of the story.
In the third Rampage the only reason you don't destroy humanity is that aliens trying to take over the world provide a distraction.
Hexen II's sparse story becomes this if you play as the assassin or necromancer. The assassin wants to kill Eidolon to prove she's the best assassin of all time, and the necromancer wants to kill Eidolon so people fear him again.
The war between Mishima Zaibatsu and G Corporation in Tekken.
If an enemy in any Marathon game accidentally shoots another enemy, they will fight it out while you stand and watch. In the second game the native f'likta fight the phfor as long as you're lying low. In Infinity the A.I. Tycho controls the pfhor hunters, fighters and you, using his forces to fight against the phfor enforcers, compilers, and Durandal's humans planned by you to keep a monster under wraps.
In Myth: The Fallen Lords the dark leaders, the fallen lords, hate each other more then they hate you. In one level you sit back for most of the level and let the two forces fight each other, then pick off the pitiful remnants.
The Mega Man Legends Spinoff The Misadventures Of Tron Bonne have you controlling one member of the main series' Goldfish Poop Gang and her Adorable Evil Minions trying to pay her brother's ransom. Sure, the main antagonist is an evil bastard trying to rule the world and your motive is quite noble...but you still accomplish it by robbing livestock from a farm, stealing containers from the docks, and blowing up a bank while fighting the police.
Legends itself has shades of this trope. The Bonne family are a group of pirates who are trying to steal some treasure from the island, and who have no problems with destroying residential areas or the mayor's office with giant robots, but they still go against Juno by freeing Megaman from his trap. Also a case of Even Evil Has Standards, given that they're obviously disturbed by Juno's plan to kill the entire population of the island.
In Fahrenheit you have two factions fighting over one little girl who could give them the power to rule the world. First you have the Orange Clan, an ancientorganization who already control the world, but wish to expand their power. The second is the Purple Clan a group of artificial intelligences who wish to use the girl's power to create a new ice age, killing humanity, and becoming the new dominate race. In between these two you have the hero, Lucas Kane, the Unwitting Pawn of both groups, who has power over The Force, and later gets killed, and brought back as The Undead.
Generals is the only game to avert this trope. The Americans are (of course) the good guys, and the Chinese are depicted rather sympathetically as well. The GLA terrorists, however, are very evil and both the Americans and Chinese team up against them.
A good many of the members in the Organization of Kingdom Hearts: Chain of Memories are working against each other in order to further their own individual evil agendas. Then in Kingdom Hearts II, Maleficent and the Heartless take on the Organization and the Nobodies. When the Organization takes control of the Heartless, Maleficent then has to pull an Enemy Mine with the main heroes.
Throne of Bhaal, one part of the Watcher's Keep involves a maze with three stones needed to escape, and two factions of warring demons, on opposite sides of the Blood War, hold one stone each. You can kill one of the factions and claim one stone off them while taking the other as a reward, or you can kill both of them. If you are a good-aligned character, you will have no choice but to kill them all — the leaders of both sides will sense your innate goodness and try to kill you.
The main story line of the game allows you to pick an evil character and do horrible things on your quest to achieve ultimate power and rule the universe with an iron fist, tormenting mortals.
Pokémon Ruby and Sapphire has a borderline case, with the two terrorist teams, Team Aqua and Team Magma. It's borderline because the teams are something of well-intentioned extremists, wanting to expand the sea and land for the sake of Pokémon (or so they say), respectively, and are in direct opposition to each other. However, in Ruby, Team Aqua are actually allies (and vice-versa regarding Magma and Sapphire), but it's played straight in the third game, Emerald, where both teams were portrayed as antagonists to the player while still warring against each other.
While Dragon Age II is mostly Grey and Gray Morality, the final conflict between the Templars and the Circle of Magi in Kirkwall devolves into Evil Versus Evil. The leaders of both factions give into their (figurative) inner demons and nearly drag the rest of their members down with them. No matter which side you initially pick, you end up killing both of the leaders to achieve a cease-fire.
Probably more 'grotesque monstrosity versus grotesque monstrosity,' but Killing Floor occasionally has instances of zeds fighting each other. This is sometimes relatively even (a Siren versus a Bloat), and sometimes comically one sided (a Clot standing in the way of a Fleshpound). Notable for the fact that, if left alone, they will gladly spend quite some time attacking each other and will often ignore players, even those who are two steps away and pointing a rocket launcher at them.
The scrolling shmup Terra Diver makes players mercenaries working for a greedy megacorp of resources around Earth against its rival corporations with the story of eco-terrorist threat as a cover-up of the disastrous war of greed.
Weaponizing various "evil" forces/creatures to send against invading goblin sieges is a popular pastime.
No More Heroes is this. Travis isn't really such a great guy, and is tearing through mobs of mooks and taking assassination side jobs on possible not so evil people all for the sake of getting laid. Once. Although a few of the other assassins are much worse than he is. Like Destroyman. And Bad Girl.
Killer7 takes this trope, mixes it up, and paints a pretty psychedelic picture with it. Some of the villains are just so awful, but a few of them are probably better than the main characters who are only doing any of this for the sake of a paycheck. Or maybe not. Some of the members of Killer7 are assholes or cowards. Barely anything makes any sense in the plot of that game.
Though one could hardly think of the title character as evil, the page describes the premise of Sly Cooper almost perfectly: a Gentleman Thief who steals from other criminals.
Uncharted 2's second half of the game sees Lazaravic's soldiers fight the Guardians Of Shambala.
inFAMOUS can have the player invoke this - if the player takes Cole down the villainous path, the final battle with Kessler becomes this until The Reveal that Kessler's actually Cole from an alternate future, who became a Well-Intentioned Extremist & travelled back in time to ensure that Cole was prepared for & able to avert the tragedy that would set him on this path in the first place. So with that in mind, it's more of a subversion.
inFAMOUS 2 features anti-Conduit fascist rednecks taking on mutants who happen to be created by the conduit power of the aforementioned anti-Conduit fascist rednecks. But it escalates even further than that, as after a third of the game another faction - mercenaries with ice powers - enter the fray, and like it's predecessor, the player can invoke this by taking Cole along the villainous path.
In Fallout 3, the cruel Talon Company (see ruthless mercs) go toe to toe with super-mutants.
The backstory of Fallout was this. The Alternate History starting after World War II had Middle Eastern powers go to war with Europe. This caused a huge economic crisis. Europe collapsed and became a war torn hell hole, and the US and China tried to solve their oil problems by invading their neighbors (in the US's case, Canada). Eventually, these last two functional governments went to war, which started in Alaska and spread to the Chinese mainland, causing China and the US to nuke one another and bring about The End of the World as We Know It. At the time of the war, China was an imperialistic, aggressive, tyrannical nation with an army of Sociopathic Soldiers. The United States was the exact same, except ruled by a puppet government controlled by a Nazi-esque Ancient Conspiracy called The Enclave in addition to all of that.
The Enclave's very existence speaks volumes about how bad the US got. The risk of nuclear war over the world's remaining oil was considered high enough to create the Enclave for continuity of government. This means the pre-war government considered billions of lives an acceptable thing to gamble for some dead dinosaurs, and this is after they'd developed fusion power anyway.
Somewhat deconstructed in Planescape: Torment, where the Blood War between the devils and the demons inevitably gets mentioned. You might think it's okay for the very, very nearly always lawful/chaotic evil beings to slaughter each other, but the suffering the war causes around the multiverse is so great that the Knight Templar angel Trias thinks allowing it to continue is an act of supreme passive evil on part of his fellow Celestials.
A late-game quest becomes this in Might and Magic VII if one goes for the evil path. You work with/for guys who want to take over the planet through force of superior weapons technology, and who find nothing wrong with mad laughter (and your personal chronicler finds the discovery of left-over torture instruments from a previous occupant of your castle to be a happy surprise). You still get sent to kill the Kreegans' King Xenofex, though, because the Kreegans are Planet Looters and a big threat in general.
Both sides of the civil war in Far Cry 2 talk a good talk about how they're making their country a better place, but both are willing to commit war crimes for tactical advantages or petty vengeance. Some of the mercenaries profess idealistic motives, but all of them except the protagonist choose money over decency. The Underground is well-intentioned, but completely ineffectual, repeatedly requiring the protagonist's help to wipe out hostile mercenaries. The closest thing to a heroic figure is the arms dealer supplying both sides, and that's only because he wants them to wipe each other out.
Metal Gear Solid V: The Phantom Pain seems to be shaping uo to be this, as the story will deal will Big Boss' fall from grace from the noble soldier he was in Snake Eater, Portable Ops, Peace Walker and Ground Zeroes, into a broken warmonger out for nothing but Revenge, going against XOF, the organization that took everything away from him on Ground Zeroes, as well as Cypher (aka, The Patriots).
Metroid Prime 2: Echoes has three enemy factions that all want the Phazon on planet Aether to themselves: The Ing, the Space Pirates, and Dark Samus. The Pirates are the butt monkeys, most of the ones that aren't killed by Samus are either possessed by Ing or killed defending their Phazon from Dark Samus. At first it's unclear if the Ing and Dark Samus are allies or enemies, but a scene just before the second fight against Dark Samus shows her killing a group of Dark Pirate Troopers (Ing-possessed Pirate Troopers) and taking their Phazon.
In Odin Sphere, most of the villains are fighting against each other and the heroes are either third parties or unwitting pawns. Ingway is running a complicated scheme of deceit and backstabbing intended partly to prevent his own cursed death. Odin wages war on the other nations of Erion and wants to claim the power of the Crystallization Cauldron for his own benefit; Fairy Queen Titania wants to keep the Cauldron out of the hands of Odin or anyone else, and both monarchs have ambitious would-be usurpers scheming within their respective courts. Queen Odette of the netherworld wants to claim Oswald's soul and punish those who dare to come and go from her realm while still alive (which is basically the entire cast). Fire King Onyx wants Gwendolyn for his wife and is willing to resort to abduction and murdering the hypotenuse in order to make it happen. The Three Wise Men seek to bring about the end of the world and release the monstrous King Gallon from the Netherworld in order to take power in the new age that follows. King Valentine is batshit insane and trying to end the world in an effort to end his own suffering, and practically every last one of them wants revenge on Odin for one reason or another.
PAYDAY: The Heist has you playing the role of four heisters who are out to make millions by stealing whatever is hot. Twice in the game, the crew go after another group of criminals because they hold something of value. In Panic Room, the crew attacks a local street gang in an apartment complex that sells drugs because the gang has a large stash of money locked in a room. In Counterfeit, there are two people who are secretly working together in making fake money with printing plates, so the crew disguise themselves as a pool repair business so they can rob the counterfeiters of the plates.
Gyral and Dalen of Fire Emblem Awakening, while not technically evil (just mercenaries), are still causing more trouble for the local population because of their petty squabbles. Chrom and company decide the fastest way to end the conflict is to pick a side and finish off the other group.
Or, you can Take a Third Option and fight both at the same time. This will cause them to Enemy Mine against you and you'll have to face a really large mercenary army against you. On the other hand, you are allowed to visit all of the villages and obtain items from them should you take this option; since taking sides in this conflict will cause some villages to close the doors on you.
It's by no means uncommon to find this trope in Final Fantasy games.
During the first half of Final Fantasy VI, the Empire is the prime villain; an oppressive, tyrannical regime experimenting on sentient beings (Espers) to gain more power. Eventual Big Bad Kefka Pelazzo is at this point seemingly a deranged, amoral coward with Starscream tendencies. This all comes to a head when Kefka turns on Emperor Gestahl, frying him with magic and kicking him off a Floating Continent.
In Final Fantasy VII Sephiroth's presence is first felt when he cuts a bloody path through Shinra HQ, murdering the despotic corporate Fat-Cat, President Shinra. Barret even queries if Sephiroth is a "good guy" as a result.
In Final Fantasy IX, we have Kuja vs. Queen Brahne after she decides she doesn't need him. She attempts to use Bahamut on him. Kuja tanks a few blasts, praises the dragon for being able to slightly wound him, then takes control of it and Brahne finds herself at the receiving end of a Curb-Stomp Battle.
The Last of Us. Tess makes it clear in the beginning of the game that she and Joel are "shitty people." Joel outright tells Ellie that he has been both hunter and hunted. Essentially, you are not necessarily a hero in this game, but a merciless survivor who happens to be the protagonist of this particular story
The Elder Scrolls V: Skyrim is mostly Grey and Gray Morality, but the conflict between the Forsworn and the Silver-Blood family is this. The Forsworn are bloodthirsty Breton guerilla fighters who worship Hagravens, rape and murder anyone unfortunate enough to get in the path of their patrols, and will reclaim The Reach even if they have to massacre every Nord in it (they openly state so). The Silver-Bloods, headed by Thonar Silver-Blood, are a corrupt crime family who bribe Markarth's city guard, murder, brutalise and imprison innocent people, use questionable business practices to remove competition, and force defeated political enemies and Forsworn prisoners to work in their prison/silver mine. It is later revealed that they have the Forsworn's king, Madanach, imprisoned in their mine, and they use him to guide the Forsworn as a deniable asset terrorist army to further their own ends. Madanach escapes along with you and some followers, cutting down quite a few bystanders and guards on their way out, and not before vowing to return with a Forsworn army to destroy the city. As one of the Forsworn NPC says, in Markarth, "there's no innocent, just the guilty and the dead".
Mace: The Dark Age; Not every contender for the Mace is evil, but evil is not on the side of evil. Lord Deimos, The Executioner, Al-Rashid, and Taria are all horrible people, but also all at each other's throats to take the Mace from Asmodeus, who stole it from Hell to run amok. It's very telling that Hell Knight, who is also literally from Hell himself, is in all one of the nicer characters since he only wants to take the Mace back where it came from. In fact, the worst thing that happens in his good ending has nothing to do with anything Hell Knight actually did.
Dragon Quest VI actually allows the player to pull this off along with an in-story use. At one point in the game, you find a castle where a demon summoning is taking place. Why? So that the demon can be orderedto kill theBig Bad. Shockingly, the demon refuses to take orders from a mortal, and nukes the castle instead. Much later, you find the Bonus Boss of the Bonus Dungeon. If you beat him in less than 20 turns, he not only recognizes your strength, but even grants you a wish, teleporting you directly to the Big Bad and utterly and completely destroying him. Then he wishes you a good day and leaves.
Sluggy Freelance: Bun-Bun, being a Sociopathic Hero, tends to get this whenever an arc focuses on him. Particularly the "Oceans Unmoving" arc where he's pitted against a naval empire out to enslave everyone in their dimension. It's not that Bun-Bun's got any ethical objections to slavery (he takes a few himself), he just doesn't want to be the one enslaved. He still comes out as the sorta good guy, because, unlike the Navy, he's evil in a cool way. He's a frickin' Space Pirate, after all.
Oceans Unmoving plays it even straighter with Bun-Bun against his treacherous former first mate Blacksoul, aka the Bun-Bun we'd been following throughout the comic as it turns out that Captain Bun-Bun was from before the comic started.
Likewise the R&D Wars, a conflict between amoral corporations employing mad science which is fixing to turn the world into either a bare rock with a single nightmarish city on it or a literal living hell.
The "Midnight Crew" Intermission in Homestuck pits the eponymous Midnight Crew against The Felt. The Midnight Crew is a small yet dangerous gang that effectively rules their city and turn out to be Alternia's versions of the Big Bad and his cohorts though they aren't nearly as evil. The Felt is a rival gang whose members possess time related powers and take orders from an Eldritch Abomination called "Lord English".
Dragon Ball Multiverse: Some potential matches, particularly Cell vs Dabura Winner is Cell and U13 Nappa vs Frieza Winner is Frieza, but not without being one-upped by Nappa so far. There's also upcoming matches - U13 Vegeta vs Dr. Raichi, and Cell vs Bojack Cell kills Bojack and wins.
In Kickassia, It is decided that "The only way to deal with a madman is to send in another madman", despite the fact that being ruled by Dr. Insano would be even worse than being ruled by The Nostalgia Critic.
Suburban Knights: On one side, there's the Big Bad, Malachite, who intends to use the Gauntlet to rid the world of all technology. On the other side, there's Jaffers and the various folks he recruited to keep the Gauntlet safe and hidden. While Malachite is obviously dangerous (he rips a guy's heart out for watching too much television!!!), Jaffers and his crew attack the reviewers and even try to shoot them several times.
The purpose for Zhao's existence was to make Prince Zuko a villain you can cheer for. This was expanded for season two, with Zuko moving further into Anti-Hero territory and the new main villain, Princess Azula, overshadowing him in every possible category.
Ba Sing Se vs. the Fire Nation in season two. Touted as the Earth Kingdom's last great bastion against the Fire Nation's invasion, it is in fact a city with a puppet king and evil shadow government that practices brainwashing. The shadow government's leader, Long Feng, comes into face-to-face conflict with Azula near the end of the season. Azula wins, even recruiting his Dai Li agents to serve the Fire Nation.
Book 2 has Unalaq vs. Varrick. Unalaq wins by virtue of releasing Vaatu, but he never manages to lay a single finger on Varrick despite having wanted him tried. Varrick however, did not like Unalaq and figured he was up to no good, but his own true goal was to make money from the conflict, and bring the war to the entire world; indeed, despite being finally arrested by the heroes, Varrick not only escapes their grasp and survives the Book 2 finale, but is still living the high life as an inventor in Book 3.
As a Villain Protagonist, Invader Zim inevitably finds himself in this situation, once against a group of Planet Looters attempting to steal Earth, once against another Irken seeking to cause The End of the World as We Know It before he could (which also required an Enemy Mine situation), and once against a crazed, overzealous mall security gaurd who imprisoned workers and customers for petty reasons and later added them to his army of zombies.
This is the Megatron/Starscream relationship. Even more explicit in Transformers Animated, where Starscream makes his break from Megatron in the first episode.
There's also Transformers Prime: in addition to the Decepticons, the Autobots also find themselves fighting the human group MECH. And on top of that, near the end of the first season, Starscream splits from the 'Cons, like his Animated counterpart. Which is then followed several episodes later by the arrival of Unicron, who's such an epitome of evil that Megatron allies with the Autobots to stop him.
Gargoyles. Oh dear God do they ever. How many times has Xanatos been betrayed or outright attacked by someone more evil than he is? And then there's Macbeth, who frequently fights against Demona.
While in Spider-Man: The Animated Series, a gang war between The Kingpin and Silvio "Silvermane" Manfredi over possession of the Tablet of Time takes place. Kingpin wants it to claim more power and influence for himself, while Silvermane wishes to restore himself back to his prime to take on the former. Kingpin's wife and Silvermane's daughter end up being kidnapped, while Dr. Connors gets caught in the crossfire and is also abducted, and Spider-Man who needs the tablet to cure himself from a disease that could end his life as knows it, has to race to stop both of them.
Tiamat and Venger hate each other so much that they tend to fight, completely forgetting about the children. In the infamous "Dragon's Graveyard" episode, the children seek Tiamat's help in trying to kill Venger.
Another example from the same series was where the kids were outclassed by an evil wizard. Presto tells Venger what the wizard is up to... queue Venger marching in to deliver a beatdown and the kids running.
In Batman: The Animated Series, the villains of Gotham City hold a very, very delicate balance between them all. The memorable Bad-Guy Bar episode "Almost Got 'Im" features such villains as the Joker, Two-Face, Poison Ivy, the Penguin, and Killer Croc playing poker, all looking like they might kill each other at any moment- and at the end it's revealed that Harley Quinn has Catwoman tied up ready to be fed into a food processor. Two-Face and Poison Ivy have an interesting rivalry, as they used to date before Harvey Dent became Two-Face. One episode shows that as district attorney, Dent had wanted to develop a park into housing, and Ivy pretended to take a romantic interest in him so she could kill him by poisoning him. This leads to a Crowning Moment of Funny, when Harvey says half of him wants to strangle her and the other half wants to hit her with a truck. Ivy then explains to the others "We used to date." Joker and Penguin immediately nod and say "Aha!" in understanding.
Conversed in an episode of Hey Arnold!. Sid suggested that he and his friends just watch two bullies, Wolfgang and Ludwig, duke it out over Gerald Field and when they're both dead they can reclaim it. This makes the example more Jerkass vs. Jerkass though, and when they try out the plan, the bullies just force the younger kids to play football to decide a winner rather than get their hands dirty. In the end, the bullies find they like each other, leaving the gang worse off than before.
Rocky and Bullwinkle: during the Kirwood Derby arc, Boris Badenov fought Fearless Leader for the Derby. When the narrator asked who would win the fight, they both turned to the camera and shouted, "What does it matter?! We're both bad guys!" The narrator admits they're right.
Two episodes of Filmation's Ghostbusters featured a villain named Big Evil, who tried to usurp Prime Evil's status as the Big Bad of that series. Both episodes invoked the Enemy Mine trope by having Prime Evil asking for help from the heroes.
The second to last episode of Justice League Unlimited "Alive!" had this. The Secret Society Grodd had created had been taken over by Luthor. However with Luthor taking much more of the cut than Grodd did and Luthor himself seemingly descending into insanity as well as not giving Tala much attention, she decided to bring back Grodd from Luthor's imprisonment along with a good number of the rest of the society who also had an ax to grind with Luthor. Luthor won in the end. And then Darkseid came along.....
Teen Titans has Slade teaming up with Robin to fight Trigon the Terible (a.k.a. Satan). He had ulterior motives. He is still Slade, but yeah, it was that bad.
Stewie vs. Penelope in Family Guy. Stewie used to be very evil in the first few seasons, but has mellowed out a lot and is more of a jerk than an evil bastard. He meets Penelope, a baby girl his age who has done her acts of killing people and having a mass amount of weapons of her own. Stewie likes Penelope at first and wants to be with her, but even he starts to have his doubts, getting tired of killing people everyday and would rather take over the world. He fights her to the death when she goes to kill Brian because Stewie wouldn't do it.
Mr. Krabs vs. Plankton in SpongeBob SquarePants, after the movie. While Plankton has always been declared a villain, Mr. Krabs rather seems to be a Knight Templar who just enjoys to give or laugh at his misery.
Evil Con Carne: The rivalry between Hector and Estroy. Also, when Hector decided to unite all villains and found the League of Destruction, all villain factions fought among themselves for control of the league. By the time Cod Commando, The Hero assigned to finish the league, arrived at their headquarters, the League of Destruction had already destroyed itself.
Eric Cartman vs. Saddam Hussein. Eric Cartman vs. Scott Tenorman. Eric Cartman vs. Osama bin Laden. The Coon vs. Professor Chaos. Celebrities vs. ginger kids in "200/201" (and they eventually team up).
The Wander over Yonder episode "The Picnic" opens with Lord Hater fighting Emperor Awesome over the chance to be blessed with cosmic power. The former is a Card-Carrying Villain obsessed with expanding his empire across the universe while the latter goes to planets and parties hard enough for them to explode.