1632: The Thirty Years' War is as a conflict between two sides who aim to kill each other.
In Animorphs, Visser Three and Visser One are usually at each other's throats — Visser One has the higher rank and Visser Three isn't secretive about how much he wants her spot. 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 that at least some of them are human). In one book, the Animorphs, Visser One, and Visser Three each had their own plans to kill off the other two at once. The two Vissers also have opposite plans about how the conquest of Earth should work: Visser One, who started the invasion, favors the slow, secretive route, while Visser Three wants to go into open war and just round up whatever humans survive the mass slaughter that will ensue.
In the first book of the Beka Cooper 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.
Much of Glen Cook's 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.
In The Book of Lost Things both the Crooked Man and the Loups both want David for their own reasons.
The final battle of the Book of Swords trilogy is fought between Yambu, the Silver Queen, Big Bad of the first 2 novels, and Vilkata, the Dark King of the third book. Interestingly, Yambu only does her Heel–Face Turnafter she wins the battle but loses her throne. The third book does give Yambu a sympathetic backstory, including something of a Freudian Excuse. But it's not an accident that she wins the battle using Soulcutter, also known as the Tyrant's Blade, a name she acknowledges.
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.
Children of the Black Sun starts out as an invasion of Ricalan by imperialist slavers is being held at bay almost single-handedly by a very powerful Evil Sorcerer with his own agenda. A decisive victory for either one would be bad news for anyone caught in the middle. Later on, however, non-evil forces arise which rival them.
In The Chronicles of Amber, Corwin actually describes himself as "a part of that evil which exists to oppose other evil."
A Clockwork Orange: Alex is a Villain Protagonist gang leader, murderer, and serial rapist, who is betrayed by his own gang in revenge for the brutal way he asserts his leadership. His Cold-Blooded Torture at the hands of the government and the Police Brutality that goes with it means that those stopping him aren't much better. Things get more complicated when he allies himself with La Résistance after that, and they betray him by deliberately driving him to attempt suicide to give the government bad publicity, making them cross the Moral Event Horizon too. Then, the government publicly apologizes to Alex to restore their reputation... by letting him go back to murdering and raping people. While it does turn out that the entire experience has soured him on his hobby, he’s not really sorry for what he’s done.
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.
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.
Knight of the Black Rose novel sends one of Dragonlance most iconic villains, Lord Soth, to Ravenloft where he quickly comes to antagonize Strahd Von Zarovich.
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 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.
Robert Reed's science fiction novelette "Five Thrillers", published in the April 2008 issue of The Magazine of Fantasy and Science Fiction, is about a sociopath who slowly rises through the political ranks, repeatedly prevents genocides and eventually (SPOILER ALERT!) saves the human race from complete destruction, all because he is disturbingly, creepily, stomach-turningly amoral, way more than the supposed villains of the story.
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.
Glinda of Oz: Ozma and Dorothy travel to a remote corner of Oz to attempt to mediate a looming war between the Flatheads and the Skeezers. It turns out that neither side's leader (Su-Dic and Coo-ee-oh respectively) are at all nice people.
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.
Grunts! chronicles the struggle between the INCREDIBLYJerkass Light, and the at best Faux Affably Evil Orcs. And then the horde of extraterrestrial armor-plated killing machines invade the planet.
Halo: 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 ancient human known as 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 take control of 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 that different.
Many clients of Hammer's Slammers are just as bad, sometimes even moreso, than their opponents. Most of the time individual Slammers voice some objections, but ultimately the regiment as a whole is loyal to the highest bidder. Though in The Sharp End a survey team scouting out two drug cartels as potential clients decide that both of them are too repugnant to work for and decide unanimously to manipulate them into wiping each other out before sending off their report to Hammer. Which leads to the planet's government hiring Hammer's Slammers to clean house anyways.
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.
Happens in-universe in Harry Potter and the Chamber of Secrets, although it's more a case of Jerkass 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 Parselmouth and almost everyone believed him to be dark because of this, somebody (Ernie Macmillan) theorized he only defeated Voldemort to have no competition. Harry himself happens to be eavesdropping on this conversation at the time, and is absolutely livid, and tells him off in front of the whole class.
The situation between the wizarding government and centaurs as alluded to in Harry Potter and the Order of the Phoenix is a case where both sides are largely, demonstrably unpleasant with the only morally grey area being the question of which came first. On the one hand, the Ministry's laws regarding centaurs clearly imply a very unfair situation similar to that of the Native Americans with a hefty dose of implied racism, and that Centaurs do not have anywhere near as many rights in the eyes of the law as they almost definitely deserve. On the other hand, the centaurs that appear aren't the most sympathetic people themselves. The centaurs we see are shown, with only one exception, to be pathologically arrogant assholes with backwards and barbaric cultural practices and they're stirred to a murderous rage by anything even tangentially insinuating a master-servant relationship between humans and centaurs (a concept so loose that it includes a human admitting to performing a Batman Gambit in order to be rescued by them or even a centaur accepting a paying job from a human), and even the nicest one we see, the above-mentioned Firenze, says some rather patronizing and offensive things about humans in the first lesson he teaches.
Hell's Children by Andrew Boland. Though most of the characters occasionally Pet the Dog, it’s mostly Evil Versus Evil.
Everyone in H.I.V.E. Series 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. Or that there are no really competent "good guys" (who aren't in some way a product of and sponsored by evil). The actual philosophical conflict running through the series is between evil as the result of valuing personal self-empowerment over either the social contract or potential consequences, and evil measuring power entirely by depowering and disenfranchising others, with no sense of "you" beyond whatever helps you win. Looked at another way, selfishness against a particularly ugly version of selflessness. Adherents to the former make more interesting and sympathetic protagonists.
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.
Edgar Rice Burroughs' John Carter of Mars has the Therns and the First-Born civilizations. They were supposedly extinctsupremacistAlways Chaotic Evil races that secretly manipulated Barsoom's inhabitants for millenia into travelling to the River Iss in search of paradise so they could be enslaved. However, the Therns and First-Born have long clashed among themselves, with the latter regularly abducting the former's females to be taken to what is believed A Fate Worse Than Death. John Carter fights against both them over the course of the book when he is trying to expose their ploys to the rest of the planet.
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).
S. M. Stirling's Marching Through Georgia pitted Those Wacky Nazis against The Draka. Most readers end up rooting for the Nazis, because the Draka are evenworse.
Predominately in the country of Praes, we have the fight of traditional For the Evulz - Evil against the new, pragmatic Evil: for example Catherine Foundling, the Squire against her nemesis Akua, the Heiress, or the nobles at the court against the Dread Empress and the Calamities.
The Drow take it up to eleven: They have been fighting a bloody war amongst themselves for millenia. Yet, even they are willing to fight against the Kingdom of the Dead...
The video game/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.
The Yuuzhan Vong, being Scary Dogmatic Aliens bent on the conquest of the entire galaxy and the eradication of all other worldviews, cause quite a few match-ups like this. Among them;
Yuuzhan Vong vs Hutts; this actually begins as an alliance, but it doesn't last long.
Yuuzhan Vong vs Thrackan Sal-Solo, the leader of a Corellian fascist movement. This one is the other way around, as Thrackan begins as an enemy of the Yuuzhan Vong but eventually becomes the leader of the Peace Brigade, their collaborator faction.
Finally, the Yuuzhan Vong are themselves rife with internal disputes. The current Supreme Overlord only got to that position by killing the previous one; Warmaster Tsavong Lah finds himself targeted by a conspiracy of the shaper (scientist) and priest castes; Executor (secret agent) Nom Anor, after falling into disgrace, sets himself up as the prophet of a heretical religion; etc.
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.
Happens frequently during Bane's Sith training in Path of Destruction.
The climax of Dynasty of Evil sees Darth Zannah finally challenge Darth Bane for the mantle of Master.
The main villains in Somewhither is the Dark Tower, a brutal tyranny who have conquered most of the words in The Multiverse. However, most of the worlds they've conquered weren't much better, being inhabited by such pleasant peoples as evil wolf-men and sadistic vampires.
A Song of Ice and Fire generally features Grey-and-Gray Morality, but occasionally two straight up villains are thrown into the ring together: Ser Gregor Clegane vs Vargo Hoat, for example. Notably they were formerly on the same side.
In "A Storm of Swords", some of the meaner members of the Night's Watch get into an argument with wildling Craster over his poor accommodations for them. This leads to an all-out mutiny and massacre that leaves Craster and the Lord Commander dead. Craster is an incestuous, abusive rapist who sacrifices his sons and marries his daughters; but the Watchmen who mutiny are traitors to their Lord Commander and their vows as a whole, broke Sacred Hospitality, and rather than freeing Craster's wives take them for themselves. It also says something that they kill Craster over his one somewhat reasonable position (he has every right to hoard his family's own food, especially with winter coming; and poor as it is his hospitality is better than starving and freezing to death) rather than over the child sacrifices or daughter rape.
When the Greyjoys (and, by extension, the entire Iron Isles) splinter and start fighting each other, we're left grading the relative shades of midnight blue (anybody banging the drum on behalf of the Drowned God, including Aeron Greyjoy), dark green (Victarion Greyjoy's more oblivious to his heinous actions than anything else), variously hues slates (most of the Rape, Pillage, and Burn-happy Ironborn, including the fairly lightish gray Asha Greyjoy) and absolutely pitch black (this would be Euron Greyjoy, primarily — but, arguably, not exclusively). When everybody's favourite immature, smug, Jerk Jock, rapist, turncoat and murderer, Theon Greyjoy, is about the closest we get to an innocent baa-lamb in this mess (he was too busy "entertaining" Ramsay Bolton in the North to be directly involved in the family spat when it kicked off), we've definitely hit this trope.
The Crapsack World slave-cities of Astapor, Yunkai, and Meereen are some of the most absolutely awful places in a world full of awful places, lorded over by utterly vile rulers whose capacity for atrocities is both petty and grandiose. Daenerys Targaryen sacks Astapor, destroys Yunkai's army, and has moved on to deal with Meereen when she learns that the depraved government she overthrew in Astapor has been replaced with one even more depraved, not to mention incompetent and largely insane. When these rulers ask for her help because Yunkai has hired mercenaries, laid siege to Astapor, and created a humanitarian crisis worse than the one she sought to fix, her counselors advise her to ignore it. She does so, in essence because she cannot handle three cities' worth of pure evil all fighting each other at once, and chooses to focus on the one at hand.
Historically "The Dance of the Dragons" turned into this, the conflict between the Blacks and Greens over the succession. It's quite a hot topic in the fandom who had the right. However both sides committed horrific atrocities and Both Sides Have a Point. It was a point of criticism in materials such as Fire & Blood that the Greens are clearly meant to be slanted as the bad guys despite the horrible deeds done by the Blacks, such as the Blood and Cheese scenario.
Gary Seven views this as the best way to play out the Eugenics Wars, playing the superhumans against one another. His plan succeeds, they spend more time fighting each other than anything else.
Beatrix Potter employs this in "The Tale of Mr. Tod" in which the two antagonists, a fox and a badger, are enemies that end up fighting each other.
This trope gets a mention in "Thor Meets Captain America" by David Brin. The Nazis gain the upper hand by using genocide as fuel for a necromantic spell to create the Norse gods. The protagonist realises this too late to pass the message on.
Better America and the Last Alliance should go down fighting honorably than even be tempted by this knowledge … to have its will tested by this way out. For if the Allies ever adopted the enemy's methods, there would be nothing left in the soul of humanity to fight for.
In The Ties That Bind by Rob J. Hayes, the heroes are pretty terrible people but they're in a GrimdarkSword and Sorcery world so they kind of have to be. Special attention goes to the Blackthorn and Inquisitor Darkheart, who would be villains in most other S&S novels.
The Lord of the Rings: 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.
The Silmarillion: Morgoth wants to take control of Middle-Earth, Ungoliant just wants to sate her enormous hunger and attacks Morgoth when he doesn't relinquish the Silmarils. She is driven away by the Balrogs.
The Fall of Númenor: The conflict between Sauron and Ar-Pharazôn pits a power-hungry, prideful tyrant with world-conquering aspirations who leads an army of wicked people against...a power hungry, prideful tyrant with world-conquering aspirations who leads an army of wicked people. It must be noted that Ar-Pharazôn declares war because Sauron dares to call himself King of Men, a title which the Númenorean King considers to belong to himself.
The first part of The Twits deals with the evil Twit couple facing off against each other before the heroes who take them down are introduced.
The main conflict in Asi Hart's dark comedy The Ultimate Killing Game is this. It is cannibals versus some violent gangsters.
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.
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."
There's additionally the Seanchan: while they are are less expressly and all-consumingly evil in terms of the Sliding Scale of Antagonist Vileness of the series, and are convinced to make common cause against Big Bad the Shadow for the Last Battle, they are also a brutal, expansionist, hegemonic culture with a rigid caste system, who are trying to systematically conquer the world and have a value system that allows them to quite comfortably oppress, enslave, abuse, or just outright murder anyone who opposes the will of their greedy, racially chauvanistic nobility and monarchy—all out of a sense of inherited manifest destiny. They kill male channelers outright and reduce female channelers to the status of animals, and it is implied that they committed a fair bit of genocide on the Seanchan continent to consolidate their power and (in one possible future at least) are set to do so again on the eastern continent, exterminating the Aiel and possibly others. For those that aren't just killed outright, sadistic physical, mental, and sexual abuse are all shown to be on the table when it comes to breaking the will of subjects and slaves, as we see in the cases of Liandrin, Almathera, and Suroth, among others. While there are a handful of Seanchan "protagonists" who demonstrate that the Seanchan belief system is complicated and not completely devoid of a certain sense of honor, and it is also shown that the quality of life of those who accept Seanchan rule and bow to all of their cultural norms is mostly decently high, even these details only marginally soften the image of this highly tyrannical and culturally/militarily imperialistic state—and it is only by comparison to the world-ending, source-of-all-evil level antagonists that they can become "good guys" of a sort, in terms of the climactic conflict.
The Witch of Knightcharm: The bitter Slobs Versus Snobs rivalry between the Medina sisters (a pair of psychotic necromancers with chips on their shoulders and a disdain for human life) and Lily's clique (a gang of rich and privileged witches who want to use The Dark Arts to Take Over the World) is quickly shown to be this.
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.
Common in Worm. Despite the main characters explicitly being supervillains (they rob a bank and everything), they spend far more time fighting off other villains or massive worldwide threats than fighting heroes or even committing crimes. Weaver brings this up specifically when talking to highschool students about the reasons being a villain sucks. Not only do you have to deal with the heroes, you constantly have to deal with other villains trying to take your territory and resources.
, depicting a history in which Nazi Germany and Imperial Japan won the Second World War, divided the world between them and instituted a most horribly oppressive society (all Jews exterminated to the very last, Blacks and Slavs reduced to sub-human servitude, torture and child prostitution as encouraged pastimes, men making out with each other in public etc. etc.). Having destroyed everybody else, the Germans and Japanese fly at each other's throats, and by the last chapter are about to destroy each other and the entire world in a nuclear holocaust — with the plot slanted to make the reader feel this might be a good idea.