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Darksiders: In the war between Heaven and Hell, you officially serve a council that mediates the two but are really looking for who set you up and taking down anyone in your way, regardless of side. At the end you turn against the mediating council as well.
Most of The Force Unleashed's missions involve Starkiller cutting down everyone and everything he comes across, including Imperial Stormtroopers who are, at the moment, at least, on his side. This gets subverted in the second half, though. Once Galen joins the Rebellion, he never has to kill another rebel soldier again.
First Person Shooter
In The Nameless Mod Trestkon can side with the Goat cult, the Llama cult, KO/avoid all cult members he fights, or take the suggestion of Phasmatis (who considers the cult wars a hazard to civilians and compares the two to warring gangs) and just get rid of both.
Also, while the main conflict in the main quest is that of PDX against WorldCorp, Trestkon can choose to side with Ryan and bring both factions down.
The dark side ending of Jedi Academy means you must fight both the Jedi and the Disciples of Ragnos on the final mission, as opposed to fighting alongside the Jedi. This is also a case of I Can Rule Alone.
Far Cry 2 has you killing both the APR and UFLL forces , and destroying both the factions.
Mostly because both sides are headed by homicidal rapist maniacs and dirty looters, and the people you're really helping as you progress in the plot are pretty much the only force of good in the game, which of whom includes the guy you were supposed to kill.
Doing this is a perfectly acceptable gameplay choice in the S.T.A.L.K.E.R. series. You could side with Duty, Freedom, the loners, or just fuck 'em all and kill everyone you see and take all their stuff. You'll probably wind up acting close to this trope anyway, although they started it.
Hack and Slash
This tends to be Masamune's story path in the Samurai Warriors game - his modus operandi is to show up mid-battle, kick ass on both sides, and the declare himself the winner.
Similarly Lu Bu's musou mode in Dynasty Warriors 6, which basically consists of him showing up to famous battles in Chinese history and killing everybody. In the end Lu actually ends up unifying China, every other leader in the game, living and dead, allies against him in a Forever War. Naturally he couldn't be more pleased.
Armored Core 4 Answer has this as one of the endings. Instead of fighting for a cause, you can choose to side with Old King and just kill everyone who crosses your path. Turns out that the whole genocide thing doesn't really go over too well with... well, everyone. You're so despicable that the other factions pull an Enemy Mine to try and get rid of you. If you can pull it off, you end up as the last man standing, and go on to commit history's worst atrocities and kill hundreds of millions more than you already have.
To a lesser extent, several of the paths in Armored Core: Last Raven have this. The Zinaida Path in particular has the player spend the game hunting down the other Ravens rather than side with a specific corporation. It's definitely the hardest path, but it's generally beneficial overall. You still save the world and the corporation power struggle has been ended by the Pulverizers.
The suggested but presumably not realised Ultimate Nihilist Ending for ADOM, which involves neither saving the world nor becoming the new sUpReMe ChAoS gOd, but rather destroying all existence. Of course, it might as well be seen as Stupid Evil or Chaotic Stupid. Or just, you know, incomprehensible.
Shin Megami Tensei I and II play this straight, having to take out both the forces of heaven and hell to get the neutral ending. In 2 though no matter what you have to face YHWH, so while you do end up killing everyone for the neutral ending in that game, you have to take down YHWH even if you're on the law path.
Shin Megami Tensei III: Nocturne has several different neutral endings. In the first, if you fight against all three Reasons, but choose to help Yuko, you will ultimately restore the world to its pre-Conception state. In the second, if you if you fight against Yuko as well, or try to help more than one Reason, the power of Kagutsuchi is wasted by your lack of a vision and the Vortex World is doomed to remain as it is for one thousand years before fading entirely. If you complete the Labyrinth of Amala, then no matter what Reasons you were previously supporting, you officially oppose everyone now, and the game ends with you ending the cycle of creation and destruction forever and marching at the head of Lucifer's army to face YHVH.
In Devil Survivor you have the option of taking a neutral option by following Gin's route, but you'll have to do exactly the same things as in the other endings: As it turns out, you have to defeat the Bels either way. However, the ending is different; the world returns to normal and all demons and angels go away. Metatron praises you for your actions and warns you never to misuse the power you've seized for yourself.
Before that, there is a battle where you can choose between fighting the demons, the angels, or both of them. If you choose one, the other side will fight with you. What you choose in this battle doesn't have any effect on the plot, however. If you don't fight the humans as well, you get a Non Standard Game Over.
Shin Megami Tensei: Strange Journey's Neutral path requires you to kill both half-angel Zelenin and half-demon Jimenez, as well as Mem Aleph, to put an end to the Schwarzwelt. It's less extreme than in earlier games, however; you avoid having to slaughter your fellow crew (as is the case on either of the other two routes, minus the brainwashing), and you ultimately end up saving all of humanity rather than Mind Raping them into soulless worshippers or demonic savages. If anything, Neutral is the least damaging of the three endings.
In Planescape: Torment, one subquest essentially runs like this... a neighborhood is caught in a war between two street-gangs: The 'evil' gang who take money wherever they can get it, and kill for kicks, and the 'good' gang of Robin Hood Wannabes who protect the locals and look out for one another. You can side with either, and push your Karma Meter appropriately... or you can have a chat with the True Neutral guy who's standing around in an abandoned building, who asks you to take out BOTH gangs, since 'both extremes are equally dangerous'. Taking his quest-line, you basically wipe out both gangs - at once, or one after the other.
After which he tries to kill you to obtain balance. If you tell him you can't die, he relents.
In Kingdom of Loathing, there's a quest in which you fight in a war between Hippies and Frat Boys. After you defeat one side, you'll be awarded one of fourteen medals, depending on which side won and how many sidequests you completed for the winning side. Every medal boosts your attributes (from +5 to +11) and enemy item drops (from +5% to +11%), but the two stats are inversely related, and the more sidequests you completed, the higher the attribute boost but the lower the item drop boost. However, with a lot of careful planning and time-consuming effort, it's possible to finish off both sides at once, resulting in a secret fifteenth medal that provides +11 to all attributes, +11% item drops, and +11% meat drops.
Also counts as Take a Third Option, as, in the war between the Hippies and the Frat Boys, you are siding with the third group of the Mysterious Island, the pirates.
In the undersea area, you can do a quest to resolve a conflict between the Ice Skates and the Roller Skates, two gangs of fish who are obsessed with extreme sports. You can help one group or the other claim the area as their gang's territory... or help a third group, the Skate Board, drive both gangs out, leaving the area peaceful.
Both Knights of the Old Republic games present options like this, although in most cases both sides are "evil", for example, the conflict between Uthar and Yuthura in the first game or between the Exchange and Serroco in the second..
Well, not exactly. Taking Yuthura's side then pulling off a series of persuasive options yields a light side ending. But it's so much more fun to betray both of them then kill all the academy students for exp (which is not, mind you, a dark side action), which sort of makes you the epitome of an omnicidal neutral character, as you're not siding with the bad guys (killing all them) or good guys (kill someone who could be redeemed), you're just killing everything.
Double-crossing both and then mocking how their own ambition let you do so nets you quite a few light-side points.
The second game includes an example with Luxa and her boss. As both are fighting for control of The Exchange it is not darkside to kill them both.
Remaining unaligned and killing everyone is one of the options in Geneforge 2. It might actually be one of the happiest endings if you don't trigger the sanity meter..
4 has a possibly more idealistic version—you sabotage the rebel superweapon so it's powerful enough to keep the Shapers at bay, but can't defeat them permanently. Incidentally, this means you've both kept the rebellion alive and prevented the slaughter of thousands of civilians (though the attrition from the continuing war still makes this an unpopular ending.)
The 5th game lets more multiple endings in than either 3 or 4. There are two endings that are more less Omnicidal Neutral.
Specifically in the first game, Omnicidal neutral destruction gives you respect by your people. In the second game, doing it with minimal canister use is the only way to ever get on the council. The third game forbids it, the 4th game allows a third option but no actual omnicide, and the 5th game will kill you if you betray everyone to try it.
In Fallout 2 this is a possible option for New Reno, which has its own ending if you kill off all the families (the other towns have bad endings as well, but nothing that shows up only if you kill everyone).
Fallout 3 allows you to maintain a neutral karma level as opposed to being good or evil, and even has one perk that requires you to be neutral.
New Vegas lets you either work with the factions in the game achieve their various ends, or screw them all and take control of the city for yourself.
The Lonesome Road DLC has the Courier intercept an armed nuclear missile aimed at the NCR. He can leave it be, attempt to disarm it, reroute to Legion territory...or launch another one, so that the innocent civilians of the NCR and the Legion are purged with nuclear fire. Omnicidal Neutral, indeed.
In a Non Standard Game Over for the Dead Money DLC, the Courier can join Elijah in using the Cloud to kill everyone in the Mojave.
In fact, Yes Man was created with this trope in mind so that an omnicidal player would still have a way to reach the endgame since Yes Man himself is an AI that will simply upload itself to another Securitron if killed.
Likewise in Old World Blues, you can either reason with Mobius and the Think Tank, or wipe them out.
At the end of Vampire: The Masquerade - Bloodlines, the player has to choose whether to side with LaCroix, Strauss, Nines, or Ming Xiao; which choices are available depends on their actions up to that point. They always have the option of siding with nobody and taking out both the Camarilla and Kuei-Jin.
Arguably, this is the only option that allows you any sort of freedom. The entire game has you basically playing puppet to everyone. Only at the end of the game, by deciding that they all need to die, can you finally give them the finger.
In Vampire? No way. You're always playing into someone's hand. In this case, you end up helping Nines, you just don't stick with him when it's over.
While the Anarchs DO end up better than the rest no matter what YOU do, you've mainly helped Smiling Jack and his "mysterious friend" even before the game's over. Really, other than the Kuei-Jin ending (where you obviously don't destroy the Kuei-Jin), there isn't much difference power-wise no matter what you do.
In the first Neverwinter Nights game when you get to Luskan the city is torn between two people fighting for control of it, each of whom will pay you to kill the other. It's kind of fun to go between them multiple times telling each the other made a better offer, eventually killing one, getting paid for it, then breaking into their base and killing them too.
The game itself can encourage this behavior simply because of the limited amount of enemies in the game prevents Level Grinding. If you want to level up fast then you kill someone's enemies, then come right back and kill them for the experience too.
Luskan captains are murderers and rapists and the player has option to save their captives so good characters also have motivation to kill both.
Mount & Blade has five factions. The player character can join any of them, champion an exiled contestant to any of the five thrones, or just take over the world himself.
Ultimately averted though when the manual specifically states that it's impossible to actually crown yourself king as none of the other factions will accept an outsider on the throne. You can still basically take over the world, though.
Now with the Warband expansion, they can recognize you as king. And you can either hire other lords, or just stay entirely neutral and make your companions your lords.
Der Langrisser has the Independent path. In something of a subversion, it's probably the least evil of all the paths.
Gothic 3 allows you to end the conflict between good and evil by killing both the good king and the bad king, then using their MacGuffins to sever the link between the mortal plane and the realm of the gods.
Might and Magic VII featured a war between the elves and the humans over your territory, during which you could choose to side with neither and battle for your country's independence. This, of course, had no effect on your later option to choose between the path of good or evil.
It does affect your personal historian's musings on the future on the evil path: suggestions of brutal warfare between the elves and humans resuming at some future point are replaced with an assurance that independent Harmondale doesn't have any obvious threats to its independence this time around.
Alpha Protocol allows you to customise your play style and personality to fit your mood. You can either befriend everyone, befriend some and use them against others, or just piss of everyone and mow through them like a buzzsaw - the latter earning itself the nickname "Dick Mike".
This is what happens in the German RPG-Maker Game Vampires Dawn 2 in the Evil/Difficult ending: the hero willingly lets himself get possessed by an evil spirit sent by the Big Bad, then slaughters his two teammates (who he holds a grudge against for turning him into a vampire without his consent and who he normally couldn't kill because vampires can't kill their sires), then drives out that spirit by sheer will, takes on the Big Bad and his Dragon, then claims the Artifact of Doom and kills the last of the other three main characters when she attempts to stop him. Then he uses it to travel back in time and start a new life instead. It's generally considered one of the best endings in the game, in part due to being sort-of canon and also featuring The Reveal of Narrator All Along
The "Soldier's Peak" DLC for Dragon Age: Origins can end with you slaying the blood mage Avernus on behalf of a demon, slaying the demon on behalf of the blood mage, or killing them both. Which path you choose will, if you import your Origins game, have an impact on Dragon Age II.
For Hircine's quest in The Elder Scrolls V: Skyrim, you are required to either hunt Sinding, a werewolf, then skin him and turn his hide into a suit of armor, or protect Sinding from a group of werewolf hunters, which nets you Hircine's Ring (and lets you tranform into a werewolf without the usual one transformation per day limit). It is possible, due to a bug, to protect Sinding from the hunters, kill him and claim his hide, then receive the ring as though Sinding was still alive.
If you ask Clavicus Vile to end the Civil War in his quest, he'll say that if he had his full powers, he could simply kill everyone in Skyrim with a snap of his fingers. War over.
Mass Effect 3's original three endings were Destroy (the Reapers, Geth and all other AIs are destroyed), Control (Shepard takes control of the Reapers and uses them to protect the galaxy) or Synthesis (Shepard sacrifices themself so that organic and synthetic life are merged into a new state of being). The Extended Cut adds a fourth option that fits the Omnicidal Neutral trope: Shepard refuses to choose from the options presented. The Reapers complete their harvest of the galaxy and are defeated in the next cycle due to the information Shepard and their crew left behind.
Turn Based Strategy
Fire Emblem Awakening has one Paralogue where you stumble upon two rival armies about to battle. Both ask you to ally yourself with them against the other. You can choose to assist either side, or you can Kill 'em All.
In the Fall Of The Samurai expansion for Total War Shogun 2, once your clan crosses a certain fame threshold, you can take the lead of either the shogunate or the imperialist faction...or you can say 'screw it' and proclaim yourself the sole rightful ruler of Japan.
Wide Open Sandbox
Way of the Samurai 3 allows the player to do this. By refusing to cater to any of the four factions in the game, you can choose to fight for or against them all. Or Kill 'em All. Literally. You can choose to kill every single person in Amana, and it's a legitimate if hidden ending for the game.
In FAMOUS and inFAMOUS 2 has a special kind of this. Capturing bad guys will get your karma-o-meter to hero, killing civilians will make your karma go red and you'll be attacked by both civilians and mooks, but killing the mooks alongside the civilians will provide you with more bad karma and get you loathed by everyone in the world, making you an omnicidal not-so-neutral.
In the X-Universe, once the player has essentially become a NGO Super Power, it's possible to effectively wipe out an entire race, though doing so isn't particularly recommended because it brings the game's economy crashing down unless you fill in the eliminated race's lost production. You can wipe out everyone besides the Kha'ak. On the other hand, the game will slowly try to bring the race back by spawning in space stations and ships, though the Sector Takeover Game Mod allows you to truly wipe out a species.
Non Video Game Examples
The Book of Swords trilogy by Michael Moorcock, telling the tale of Corum, the Prince in the Scarlet Robe. The books tell of Corum's war against the Lords of Chaos in favor of the Lords of Law, often invoking the Cosmic Balance. At the end of the last book, he manages to involve the God-Brothers Kwyll and Rhynn, who are not bound by Order, Chaos, or the Cosmic Balance. In gratitude for a favor done, they kill off the Chaos Lords. Then (just for the lulz) they go on to kill off the Law Lords as well, negating the Cosmic Balance by default, and leaving the mortals in control of their own destinies, with no interfering gods to muck things up. A happy ending.
The Green Anarchists' motto from the Russian Civil War: "Beat the Reds until they become white, beat the Whites until they become red".
Keith Laumer's Dinosaur Beach demonstrates an extreme, but ultimately heroic, version of this trope. The setting has been deeply screwed up by the invention of time travel, with each faction trying to prevent any time travel in its "future," but at the same time trying to prevent the prevention of time travel in its "past," since all of them are the futures of factions that were unable to prevent time travel, and none of them wish to be erased from the timestream. Meanwhile, each time trip is making the fabric of reality less and less stable. The main character's solution is to travel back and prevent the invention of time travel, preventing the collapse of the universe at the cost of the lives and existences of every member of every faction in the book. He's one of only two characters, named or unnamed, who comes from a future timeline but still exists at the story's close.
Possible Real Life example: Governor Nelson Rockefeller's reaction to the Attica prison riots.
In an example similar to the page quote, Russel Sharp of XSGCOM believes that his best chance of getting into heaven is if God doesn't want him on Satan's side. Another character agrees with him, saying that it would "require a rewrite of Revelations." In-series, he fights for Earth... and really, only Earth. He has shown that he doesn't really care about Earth's off-world allies, and considers all non-earth humans to be below him. At one point, he's tested to see if he was the one who ordered attacks on the Free Jaffa and Tok'Ra, and he's more annoyed by the idea that they thought he would leave survivors "like an amateur" than the idea that he was behind the attacks.