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Anime and Manga
- The entire premise of Strike Witches for World War II. Instead of World War II being fought against each other, it's against the Neuroi Alien Invasion.
- Kyoji Mujo from Scryed managed to take over the story entirely, burying the whole Kazuma vs. Ryuho rivalry until the final episode.
- Same with the Overdevil from Overman King Gainer. The final scene of the series is practically a Lampshade Hanging: "er, guys, weren't we supposed to be headed to Yapan instead of dealing with Eldritch Abominations?"
- Piccolo and Son Goku's rivalry in Dragon Ball Z effectively ends when the arrival of Raditz, Nappa, and Vegeta force Piccolo into a Heel–Face Turn. Vegeta himself shortly afterwards teams up with the heroes to take on Frieza and the Ginyu Force.
- Also, Cell, who was introduced shortly after the androids were introduced, ends up becoming the Big Bad of the arc. His case is more unique in that he establishes himself by absorbing the androids to get them out of the way and power himself up, rather than the androids making a Heel–Face Turn to fight him with the heroes (although that does happen after they manage to make Cell regurgitate one of the androids).
- The Water Seven storyline of One Piece seems to set up Franky as that arc's big bad by having him and his goons beat Usopp to a bloody pulp. The Strawhats vow revenge and tear Franky's henchmen a new one, causing HIM to swear vengeance in turn...it all seems to be leading up to a big showdown between Franky and Luffy, until the Wham Episode which turns the plot on its head leaves our heroes with much, much bigger problems to worry about. Franky does a Heel–Face Turn and proves to be far more interesting as a good guy, anyway. And ultimately ends up joining the crew.
- In Mahou Sensei Negima!, this is how Tertium treats the other Fates, tell them that upstarts who show up out of nowhere to steal his prey is grating on his nerves. An unusual villainous example since to the heroes, this doesn't make a lick of difference, they're still fighting for their lives against impossible odds.
- In Alive: The Final Evolution, the three way conflict between the American government, the alien Mitama and her followers, and the protagonists over possession of the "Heart of Akuro" gets derailed near the end by Hirose, who was given the Heart on the assumption that he could be easily manipulated. With the Heart making him the strongest thing on the planet, Hirose ignores the secrecy all the other factions were fighting under in favor of single-handedly launching a war against everyone else on the planet. The previous conflict between everyone is put aside in order to stop his attempt to commit genocide on all of humanity.
- In Transformers: Generation 2, it seems like the coming of the Swarm (hinted by visions Optimus Prime had) will end the conflict between the Autobot-Decepticon Alliance and the Cybertronian Empire, but the trope is averted when Optimus tries to reason with Jhiaxus to work together against the Swarm, since Jhiaxus responds trying to kill Optimus. Besides, after Jhiaxus dies and the menace of the Swarm is over, the Cybertronian Empire still exists at the far reaches of the universe, led by The Liege Maximo.
- The third X-Force run started out as Wolverine's team of black ops killers taking out the evil Purifiers, but they got sidetracked not once but twice - first, the villain of the Cable series shows up and the team goes on a merry chase through the timestream after him, and second, a minor character from the first story arc goes to work for a would-be goddess previously unseen in the series. Both times the Purifiers plot is put on hold, and as a result the threat they pose builds into the next Bat Family Crossover.
- Post-reveal Wilhelm Kriegsen from (On the) Path of Vengeance, possibly reprising this role in Endless Waltz.
- In Changing Lanes, the two man rivalry between Ben Affleck and Samuel L. Jackson is put aside when they both decide to go after Sidney Pollack, thus eliminating the violent escalations that defined the movie up to that point.
- Cowboys and Aliens begins with a fairly standard Western conflict between a cattle baron and the local law, but gets derailed by the sudden appearance of aliens. The two sides join forces to attack the aliens and renconcile their differences. Later on, the coalition runs afoul of a Native American tribe and a bandit gang. These conflicts are also killed by alien attacks, and all four factions ultimately end up cooperating.
- Hard Rain twists in the third act as the police force turns on the protagonist and the villain, forcing them to team up in order to survive.
- The Culture novel Matter replaces the inheritance conflict between the Princely Young Man and the Evil Chancellor by having them both be nuked by some world-destroyer only slightly implied in setting fluff. Later much of the cast is killed at the end of the book as they just barely defeat it, without showing the moments directly following. Finally a single page in the epilogue implies how the government restructuring was finally resolved without going into much detail. This keeps with one of the main themes in Matter about inter-galactic politics and interactions between different tech-level species. The inheritance conflict was very important to the people living in the empire, but insignificant to the rest of the galaxy. This sequence was set-up as a Wham Episode to show how none of it really Mattered in the end.
- Isaac Asimov's Foundation series has the Second Foundation attempting to shorten the length of time the Empire collapses to a thousand years when "The Mule" arises, derailing the Plan-scheduled civil war by having the Traders and Foundation proper join up against the threat of the Mulenote .
- In the Codex Alera series, the Vord serve as this, allowing a lot of Enemy Mine opportunities in the later books due to the cleverness of one of the characters.
Live Action TV
- Buffy the Vampire Slayer:
- In the fourth season, Knight Templar and Manipulative Bastard Maggie Walsh was replaced as the Big Bad by Frankenstein's Monster Wannabe Adam in the second half of the season, turning an interesting "do the ends justify the means" conflict into an excuse for the heroes to turn into some spirit magic version of Voltron.
- Season 2 did this twice. Season 1 ended with the Anointed One, a sort of Vampire Messiah in a child's body set up as the new Big Bad. That was awesomely undone when Spike showed up and started his plans to reassemble The Judge. Spike vs. The Slayer was later taken over when Angelus appeared in the middle of the season.
- Also happens when Willow goes Woobie, Destroyer of Worlds and kills Warren in Season 6. Buffy is fond of this trope.
- Happens yet again in season three, with Mr. Trick, a clever vampire crimelord who gave Buffy a great deal of trouble early on in the year, getting abruptly staked by Faith, just in time for her and The Mayor to step in as the real villains of the season.
- By then Mr. Trick had already become The Dragon to The Mayor, Faith just replaced him in that role.
- In the third season of Deadwood, Hearst enters town and forces an uneasy alliance between Bullock and Swearengen.
- Happens in Stargate SG-1 when the Replicators start destroying the Goa'uld, suddenly fixing the problem the heroes have been dealing with for the past 8 seasons. This also forces them to work with Ba'al to destroy the Replicators, but they go back to being enemies shortly thereafter.
- Occurs in Stargate Atlantis when the Replicators start to attack the Wraith by attacking humans (the Wraiths' food source). Atlantis teams up with Todd and his Wraith to destroy the Replicators, but they do resume their regularly scheduled conflict once the Replicators are dealt with. An interesting example in that the Atlantis team intentionally created their own conflict killer by reprogramming the Replicators to attack the Wraith. They didn't expect them to try to starve the Wraith but they did get (almost) what they wanted.
- In Star Trek: Deep Space Nine, the introduction of the Dominion rapidly took over the entire series, spanning the entire rest of the show's run at the expense of most episodic plots.
- Played straight in the final episode of the second season of Star Trek: Enterprise. The Xindi take over the story for the next full season.
- This happened a few times in Lost. Ben Linus's nemesis Charles Widmore brought about an Enemy Mine situation with the 815 survivors and the Others. Widmore became the off island Big Bad in season 5, which also revisited in detail another faction in conflict with The Others that had only made a few scattered appearances beforehand. A handful of 815 survivors became this faction's enemies in the final stretch of that season while the Linus/Widmore conflict was put on hold until near the end of the sixth and final season. The season 5 finale introduced two characters who had been alluded to for some time, but who had never been portrayed by actors until then, and their conflict became the focus of the final season.
- Season 4 of Prison Break has almost everyone team up against The Company. Michael lampshades the situation by saying "there's a lot of history in this room".
- Scorpius of Farscape: he shows up near the end of the first season, usurps Captain Crais and forces him to run off to the heroes to save his life. Doesn't completely end the conflict, given that Crais and the crew of Moya are still at odds for most of the second season- just for different reasons.
- In the first season of Hikonin Sentai Akibaranger, the Akibarangers and Malshina work together to resist Executive Meddling.
- Warhammer 40,000 was originally a conflict between the Imperium, the Forces of Chaos, Orks, Eldar and Tyranids. Then in the 3rd edition they added two armies, the Dark Eldar and the Necron and attempted to cram the Necrons in as the new Big Bad. Games Workshop also attempted to add the Necrons in as a mysterious, subtle horror, which doesn't always work in a universe about as subtle as being bludgeoned with a Gwar concert.
- This said, it has to be taken as a growth from being Warhammer INSPACE! to being it's own work. The game is a far cry from being Rogue Trader. (The original game, not the RPG)
- BattleTech at first it was the Inner Sphere against each other, then the Clans come in between them. Then years later the Word of Blake becomes the main opponent for everyone.
- In AT-43 the arrival of the Therians in Ava prompt the UNA and the Cogs to temporarily join forces against them.
- In The Legend of Dragoon The apparent villain is your father, thus giving the characters a great, morally conflicted enemy. Then it turns out your father was being possessed and controlled by the Sealed Evil in a Can.
- Double duty. That sealed evil, upon revealing himself, hijacks the body of the Virage Embryo in Shana's place, saving Dart and Rose from having to mercy kill her themselves.
- Subverted and Lampshaded in Command & Conquer 3: Tiberium Wars with the introduction of the Scrin, who note that the two factions (Nod and GDI) are continuing to fight each other while battling the Scrin invasion.
- Played straight in the Allied campaign in Yuri's Revenge, where the reveal of Yuri's treachery and the fact that he has built up an army of his own leads to a cease fire between the Soviets and the Allies. The Soviet campaign instead has them stealing Allied technology to quickly alter history and win the war, then turn their attention to dealing with Yuri.
- Martinez in Grand Theft Auto: Vice City Stories is an annoying example, where he interrupts the plot near the end, thinking that the player is the same nobody he pushed around in the beginning, despite the player at this point having taken out Martinez' boss' boss' bosses, and can buy and sell his entire racket millions of times over.
- Arkham from Devil May Cry 3: Dante's Awakening, even though the brothers teaming up was one of the series' (many) awesome moments. Vergil later lampshaded it before the duo get back to dueling each other:
Vergil: Well, you don't possibly believe that he deserves to be our main event, now do you?
- Star Ocean
- Jie Revorse in Star Ocean for SNES/SFC. In the PSP remake, this is much better handled and explained and he no longer comes out of nowhere.
- Star Ocean: Till the End of Time. Fayt is stranded on a backwater fantasy planet with no way off, and the main conflict is a fairly standard fantasy world war between religious matriarchy Aquaria and hostile, warlike Airyglyph, until the plot from the beginning catches up to him, and the space fleet that attacked the planet he was previously on comes to the backwater fantasy planet to attack it. The two countries realize they have to join forces, and Airyglyph as a country is revealed to be not that bad (it helps that the warmonger who'd been driving the conflict got killed in the attack).
- In Jak II: Renegade, the main villain at the start is set up as Baron Praxis, who Jak has sworn to get revenge on. They fight twice, but the Baron is never really defeated. Near the end, he is killed by the real Big Bad, the Metal Head Leader, who we had only seen fleetingly until this point in his true form at least.
- Subverted in Dragon Age II. The Arishok seems to be this for the mage-Templar conflict in Kirkwall. He's the military leader of the most alien faction in Thedas (physically and philosophically), and it takes both sides working together to stop him once he's been provoked. However, that's just the second of the game's three acts - afterwards, the prior conflict resumes. He indirectly *worsens* tensions by killing the Viscount, leaving a power vacuum for the Templar leader to fill.
- Final Fantasy
- Final Fantasy VI spends the first half of the game focusing on the conflict between The Empire and the Returners, before Kefka, formerly The Dragon, reveals that he has his own apocalyptic ambitions. The Emperor belatedly tries to stop him, but Kefka proceeds to settle the the conflict by destroying both sides, along with most of the world, and setting the stage for a final showdown with him instead.
- Final Fantasy VII would go on to use much the same plot structure. The first part of the game seems to be a struggle between La Résistance and an evil Mega Corp.. Once Sephiroth shows up and goes on a killing spree through Shinra's headquarters, though, the story quickly switches tracks and he becomes the new Big Bad. The Corrupt Corporate Executive even went on to pull a Heel–Face Turn in the spinoff games, due to Sephiroth being so much more evil in comparision.
- Although it flip flops a bit. Initially Shinra is still an issue as you continue to track Sephiroth down while trying to throw them off you up until you leave the continent they are based out of, at which point they drop out of the story for a good long while barring an occasional Turk encounter. However when your party finally catches up to Sephiroth Shinra reappears again, revealing that they were tracking him as well and only stopped attacking because they had a spy in your party and therefore were marking both your progress. After this Sephiroth seals himself into the final dungeon and begins his plan to destroy the world, which will take awhile so Shinra is now the main villains again for the rest of that disc until their final defeat (and the death of the members pushing for the attack of the party the most) at which point Sephiroth becomes the villain again.
- Tales of Vesperia. One word: "Adephagos." Turned a perfectly good ethical conflict into a "stop the Knight Templar and the big bad monster thing" race with a final dungeon that came out of nowhere.
- Fate/stay night has several over the course of its three storylines. First, in the Fate route, Gilgamesh takes out Caster during Caster's sudden attack on the heroes' base and establishes himself as the new villain (he actually turns out to be The Dragon). Then, in UBW, Archer takes out... Caster... when she's about to kill them. And then... Gilgamesh kills him shortly afterward when it turns out that Archer may not be all that bad. Finally, in Heaven's Feel, the Shadow and True Assassin practically ruins the whole Grail War by dropping bridges on all the Servants except Rider. The one that the heroes first discover? Caster.
- In Fire Emblem: Radiant Dawn, Part 3 is a war embroiling most of the known world, stopped short by the awakening of a god. It had been foreshadowed since the previous game that such a war would cause this to happen, and comes right in time since the player controls both sides of the old conflict.
- The beginning of Super Mario RPG, where instead of a normal "Mario defeats Bowser" story, the two rivals join forces to defeat a giant sword.
- All three Mario & Luigi games begin with Mario battling Bowser in Peach's Castle to stop him from kidnapping her, just before they find out about the true villains.
- Early in Clash At Demonhead, you have an inconclusive fight with Tom Guycot, the apparent boss of the terrorist organization you're trying to defeat. About halfway through the game during a seemingly-unimportant sidequest, the player character is tricked into releasing a demon. Said demon promptly clobbers him and kills Guycot, forcing the player to go on a quest for a magic sword to kill the demon. You'd think the demon would then take over the plot, but in a weird subversion, you just kill it with the sword, destroy it's eggs, then go right back to fighting terrorists. The Final Boss is the guy who was giving Guycot orders.
- The first Starcraft campaign concerns the conflict between La Résistance and The Empire. Then the Zerg show up.
- This happens in Team Fortress 2 quite lirerally. Gray Mann kills his brothers Redmond and Blutarch, effectively ending the RED vs BLU war. BLU and RED end up working together in order to take him down.
- A common phenomenon in many strategy games (particularly of the Four X type) which involve multiple competing sides and a Tech Tree. What happens is that while the more active players expand and compete with each other militarily, a less aggressive faction is able to sit back in their corner of the map and climb the Tech Tree undisturbed. This eventually gives them an unstoppable advantage over the apparently superior competitors when they do join in the fray. Occurs less often in multiplayer games, as humans know to team up and gank the techer early on.
- In Anarchy Reigns, Nikolai serves this purpose as the real Final Boss.
- In Godzilla Unleashed, you become this in the Tyrant ending, by becoming so powerful and insane through crystal use that everyone else's agenda has become irrelevant; either everyone takes you down or the world is doomed.
- In the majority of the Dead Space series, conflict has been with elements of EarthGov primarily, in terms of human antagonists. Come Dead Space 3, the Church of Unitology, which has generally served as a loosely organized collection of secondary antagonists at worst and never really come together in a united front in any significant way, band together under the Circle led by Jacob Danik, who had never been mentioned before that game. This new group has its own military and seemingly overthrows EarthGov in the opening of the game, which Isaac Clarke doesn't seem to even be aware of happening, let alone that The Government is on its last legs, until he is told up front.
- Morgan takes over Troy's role as the Big Bad when the characters' masks start to come off. Because he is hideously disfigured (chemical splash at college), he refuses to allow people to be different and forces people to wear masks like he does.
- 8-Bit Theater has what looks like a final conflict brewing between the Light Warriors and the Dark Warriors; but then the Other Warriors show up because they want to kill the Light Warriors too; but then, the Fiends show up to kill the Light Warriors as well, so they look like the Big Bads; but then Black Mage anticlimactically absorbs their power for himself which makes it seem as if he is the Big Bad; but then Sarda reveals himself as the Big Bad, (although he actually claims that the Light Warriors themselves are the BigBads); but finally Sarda blows up due to absorbing too much power, and becomes a portal for Chaos' who is the actual Big Bad. All in all there are five Conflict Killer moments in succession at the end of the comic.
- Homestuck has Jack. Usually just an NPC used as a back-door quest to bypass a difficult fight. In the kids' session he gets hold of a powerful artifact and goes on a rampage, utterly obliterating the chess-like battle between the kingdoms of Prospit and Derse.
- In turn, Jack Noir is supplanted by Lord English as the Big Bad, to the point that one character claims he's old news and barely a threat any longer.
- Following the first arc of Worm the Undersiders were just gearing up for a conflict with Empire 88 when Leviathan attacks the city, causing all of the major villains and heroes to team up to fight him, and killing Empire 88's leader in the ensuing battle. In the next arc, Coil and his subordinates are getting their plans to take control of the city from the PRT and the remaining supervillains when the Slaughterhouse Nine come to town, prompting another Enemy Mine scenario to defeat them.
- Chaotic's second season has a fifth tribe, M'arrilians, appear and change the plot from the previous search for the Cothica and fights between the tribes to the tribes working together to fight the new threat.
- The main conflict of the first season of Avatar: The Last Airbender revolved around Prince Zuko following the Gaang around the world trying to capture Aang so that he could return from his exile, accompanied by his uncle Iroh. However, Admiral Zhao steps in and proves to be the bigger threat. The second season opens with Zuko's sister Azula (who had previously only be seen in passing during a flashback and recieved a brief mention in the last episode) trying to finish her predecessor's job and attempting to arrest the two of them, forcing them to go on the run. Shortly after, Azula encounters Aang by chance and resolves to track him as well. Only one episode has Zuko still trying to capture Aang, and he still has to compete with Azula to do it. A bit more palatable then usual, as the first season had clearly ended on the fact that Zuko and Iroh had become vilified by the Fire Nation, as well as having lost the resources which would let them follow the Gaang.
- In Star Wars: The Clone Wars, when Obi-Wan and Anakin are sent to retrieve the detained Count Dooku after Hondo Ohnaka's pirates agree to hand him over to the Republic in exchange for a hefty sum, they end up being captured and used as hostages as well, and are forced to make a tenuous alliance with Dooku to escape the pirates. Ironically, when Dooku sends General Grievous to exact his revenge against Ohnaka for his earlier capture several seasons later, Hondo and his pirates then team up with Ahsoka and the Jedi younglings whom he had just stolen lightsaber crystals from to escape Grievous' forces.
- Likewise, in Darth Maul: Son of Dathomir, Dooku agrees to put aside his previous differences with Darth Maul when Republic forces arrive to capture both of them, and they jointly engage Obi-Wan Kenobi, Mace Windu, Aayla Secura and Tiplee in lightsaber combat as part of a short-lived alliance of convenience.
- ReBoot subverted this. When the Web invades Mainframe Bob and Megabyte are forced to team up. Instead of ending their conflict, Megabyte takes advantage of the situation to get rid of Bob before the Web invasion is over.
- Family Guy had a joke poking fun at this. At the beginning of "Brian Griffin's House of Payne," Peter mentions an idea he has for a "Jaws" sequel where the humans and the shark team up to fight an even bigger shark, named "Big Jaws." At the end of the episode, we find out he got it produced, and get to watch the scene introducing the Conflict Killer in question. Not surprisingly, it's awful.
- Transformers Armada at first it was usually the Autobots and the Decepticons fighting over the minicons, then Unicron comes up to attack both side.
- This occurred at the end of both Seasons 2 and 3 in Justice League Unlimited. In Season 2, Word of God states they couldn't come up with a way of resolving the conflict between Cadmus and the Justice League, so they revealed that Braniac was controlling Lex Luthor all along. In Season 3, the Conflict Killer is the unexpected revival of Darkseid, forcing an Enemy Mine between the League and the (unnamed in series) Legion of Doom.
- My Little Pony: Friendship Is Magic: The primary conflict in "Bats!" was Applejack and Fluttershy's argument over whether they needed to drive a swarm of Vampire Fruit Bats off of Applejack's family farm. Then Fluttershy gets accidentally turned into a feral batpony, and the rest of the episode is dedicated to figuring out how to turn her back.
- In the Series Finale of Legion Of Superheroes, Imperiex, who had been the Big Bad for the entire second season, is Killed Off for Real by Brainiac-controlled Brainiac 5 (much to Superman X's rage), leaving the legion to deal with Brainy as the ultimate threat instead.
- In the third season of Jackie Chan Adventures, the J team has to go through the talisman hunt again in order to keep the powers from Dalong Wong. The finale, however, ends up having the Final Battle being with a resurrected Shendu while Dalong is one-shotted in a brief scene.
- The British to the Muslims and Hindus in India.
- The Persian Empire forced the bickering Greek city-states have to work together to fight back an invasion.
- Britain and France had spent their entire histories being at each others' throats, until both realized that the Central Powers were too strong for either of them to take on alone. This led them to form the Triple Entente and later the Allied Powers.