Deus Ex: Human Revolution has an interesting one in the background. The matter of human augmentation is a topic that both liberals and conservatives can join in on. Liberals are against it because it widens the gap between the poor and the rich, whereas conservatives believe it is an affront to God to alter the human body.
In Battlezone, the Americans and (remnants of) the Soviets team up to take down the Furies (alien spaceships brought back by the Soviets). In fact there is even a rescue mission before the team-up mission, in which you have to rescue the Soviet survivors (the Furies rebelled after taking down the Black Dogs (third faction and the one used to create the Furies in the first place).
In Final Fantasy X-2, the Leblanc Syndicate, who are enemies originally, become allies of the Gullwings in Chapter 3. This is different, however, in that they remain allies for the rest of the game, even helping in the fight against Vegnagun.
In City of Heroes, in the Valentine's Day 2006 and 2007 events, the missions to unlock special prizes required mixed hero-villain teams to complete. As well, the issue 10 update included a whole hero-villain co-op zone, the Rikti War Zone.
Issue 12 added Cimerora, another co-op zone.
Finally, the annual "Rescue Baby New Year" event allows heroes and villains to team up, explicitly because the kidnapping of said baby/personification of time would be really really bad for all concerned.
Happens quite often in Metal Slug. Twice, the Rebellion teams up with you to fight the Mars People: in Metal Slug 2 when the Mars People betray them and kidnap their leader, and again in Metal Slug 3 when their leader turns out to be a Martian impostor. Even the ultimate recurring rival and badass Sgt. Allen O'Neill fights on your side. In Metal Slug 6, both groups team up with you to fight a group of Martian-eating aliens.
In the Super MarioRPGs (such as, well, Super Mario RPG), Bowser will often team up with Mario against other villains, wanting to be the only villain around. He's particularly enraged when other villains inevitably kidnap Princess Peach in the course of their plans. Or when someone has the nerve to kick him out of his own castle, like Smithy does, he's not going to let old rivalries keep him from getting it back.
In contrast with how he deals with new villains in other Mario role-playing games, Mario & Luigi: Dream Team has Bowser knowingly (as in, no brainwashing or accidental assistance) team up with the Big Badagainst Mario, even though Antasma has commandeered his role as the Peach-kidnapper, after the new villain tells him We Can Rule Together. Turns out Bowser was exploiting Antasma's extra help the whole time; he later throws Antasma under the bus to be dispatched by the Mario Bros. while he takes the Dream Stone for himself.
Halo does this twice. First, at the end of the second game, the humans of the UNSC and the Covenant Elites, who were previously mortal enemies, join forces to fight the Prophet of Truth, who betrayed the latter and was responsible for ordering the extermination of the former. In the third game, right before confronting Truth himself, the Master Chief and the Arbiter join forces with the Flood to stop Truth from killing everyone in the galaxy.
Granted, this latter alliance lasts only five minutes, but no one was really expecting the Gravemind to help you anymore than it has to. Although it did at least have the minimal grace to wait until Truth was dead first.
The full extent of the human/Elite alliance is explored in the ending of Halo 3 and a number of works released afterwards. Admiral Hood says that he can never forgive the Elites for what they did as part of the Covenant, but implies that they just might be able to ignore each other until some time in the future when the pain of the war isn't as fresh. They're not really enemies anymore, but they're definitely not friends.
In fact, certain factions of both sides are still enemies; a number of Elites still believe that humanity needs to be wiped out, and the UNSC's Office of Navel Intelligence (ONI) is actively attempting to foment civil war among the Elites. Since the Elite's current leader, the Arbiter, is actually quite human-friendly, this ironically leads to a temporary Enemy Mine situation between the anti-human Elites and ONI.
On the other hand, a number of other Elites, particularly among the young, grudgingly respect humans, despite the latter's physical inferiority, for their ability to hold out for 25+ years against a technologically and numerically far superior enemy. It helps that the Elites are a bunch of Proud Warrior Race Guys who respect honorable and skilled fighters regardless of whatever side they fight for; in fact, a number of them were puzzled that the Prophets never offered humanity a chance to join the Covenant, which is their normal M.O. If nothing else, they'd be an improvement over the Grunts.
In Devil May Cry 3, hero Dante teams up with his brother and enemy Vergil to fight the penultimate boss. It's barely cold when Vergil challenges Dante for ownership of the Force Edge.
StarCraft is full of those, especially in the Expansion Pack. It starts with Raynor being forced to team up with the Sons of Korhal to evacuate his Doomed Homeplanet and ends up with a three-way alliance between the Terrans, Protoss and Zerg against the Earth Directorate and immature Overmind they were trying to control.
In StarCraft II: Wings of Liberty, during the final arc, Raynor join forces with the Terran dominion, or at least some Dominion forces led by Prince Valerian, who explicitly does not have his father's approval, against Kerrigan. This time, it works.
Warcraft, borrowing some plot elements from StarCraft, also has quite a few such moments, the ultimate being the battle at Mt. Hyjal where the Alliance, the Horde and the previously hostile to both night elves put their differences aside to stop the demons. Only to have the Alliance (now including the night elves) and the Horde break apart in about 4 years in time for the next game in the setting, World of Warcraft.
Which got its own moments of temporal alliances, such as the War of the Shifting Sands, and the Opening of the Dark Portal (where the Horde and Alliance came to the aid of a neutral faction holding back demonic forces coming through the portal).
In Burning Crusade, there are Aldor and Scryers factions in Shattrath City which are rivals of each other on the borders of open hostilities. Players have to pick between them and befriending one means you are hostile to the other. However, near the conclusion of Burning Crusade during the Sunwell event, they finally put aside their differences and band together to form the Shattered Sun Offensive against Kael'thas Sunstrider and Kil'jaeden.
Another was added in Wrath of the Lich King, though it borders on Big Damn Heroes. The Alliance and the Horde work together at the Wrathgate in fighting the Scourge, which stands in contrast to them murdering each other for resources and fun everywhere else.
In fact, a massive part of Wrath is how the Horde and Alliance start with this and end trying to kill each other and letting the Lich King off to the side to kill them both. In Cataclysm, Deathwing has become a greater threat than the Scourge was because the Alliance and Horde have lost all pretense of working together on anything.
In "Rise of the Zandalari", Vol'jin, leader of the Horde's Darkspear Trolls, is so concerned about the Zandalar's Sudden Sequel Heel Syndrome, that he sends emissaries to both the Horde and the Alliance. Instead of trying to get Warchief Hellscream and King Wrynn to work together, he reaches out to the individual heroes, and the smaller groups within the Horde and Alliance that are directly in the trolls' path.
The opening cinematic of Mists of Pandaria has a shipwrecked orc and human trying to kill each other, then teaming up against a lone Pandaren who interrupts their fight. Doesn't keep them from getting their clocks cleaned.
Mists of Pandaria has the Klaxxi, a group of Mantid elders who seek outside help when the Sha corrupt their current empress; however, they have no intention of stopping the millenia-long war with the rest of Pandaria, and worship the Old God Y'Shaarj. If Y'Shaarj should ever return, they would serve him again, and if the players were smart they would too. When Garrosh released the heart of Y'Shaarj the Klaxxi allied with him in order to serve their god.
Garrosh managed to temporarily unite the majority of the Horde and the Alliance against him due to his actions, beginning with the Darkspear Rebellion and ending with the Siege of Orgrimmar.
The climax of the Restoration Wars featured a team-up between Catherine Ironfist and a faction of Necromancers that had gotten tired of Catherine's father's rule (events earlier in the story had lead to his reanimation at the Necromancers' hands, only for him to promptly off their king and take control himself).
Might and Magic VIII plays with it: on the one hand, the Big Bad gives you as much help as he can give. On the other hand, the only reason he is your enemy is because of a safety protocol intended to keep him from being subverted by the Kreegans (he cannot stop once he has started the destruction of a world), so him trying to sidestep it as much as is possible is only to be expected.
With the Star Fox team mostly disbanded at the beginning of Star Fox Command and Fox unable (or unwilling) to get his friends back together, one of the paths you can take has Fox hiring long time rival Wolf O'Donnel to help him defeat the Big Bad.
And going back to Star Fox Assault, Wolf helps Fox rid the menace of the Aparoids in the last four missions.
Marth and Meta Kight fighting, then suddenly teaming up to defeat the Primids around them. This happens again when Meta Knight fights Lucario then immediately after the fierce battle that manages to turn one of them into a trophy, they team up to board the Halberd. This almost happens again when they find Solid Snake, but Lucario stops Meta Knight. Meta Knight has an interesting way to make new friends...
Ancient Minister aka a R.O.B. unit helping Donkey Kong, Diddy Kong, Captain Falcon, Pikachu, Samus, and Captain Olimar.
King Dedede (by Ness and Luigi), Bowser (by King Dedede, who pointed out that there's a bigger enemy, Tabuu), Ganondorf (by Link and Zelda) and Wario (who kicks King Dedede, which King Dedede, Luigi, and Ness respond to by pointing out Tabuu to Wario, who looks uninterested. When they decide to move on without him, he races past on his bike and beats them to the Big Bad's final dungeon).
A comedic example is shown in Command & Conquer: Red Alert 3 where the three factions (represented by their respective tanks) call a truce in the tutorial in order to teach the player not to send their units to their meaningless deaths, though are still prone to firing at each other. Usually at the Soviet Hammer tank.
A more serious example is also to be found in the Allied campaign when the Empire of the Rising Sun attacks-the Allies and Soviets call a ceasefire to destroy the Empire, and proceed to betray each other at about the same time.
This also occurs in the Tiberium series. In the expansion pack Tiberian Sun: Firestorm, the remnants of Nod and GDI have to work together to stop the renegade Nod AI, CABAL. In Tiberium Wars, Nod general Kilian Qatar allies with GDI to face off against the Scrin, until Kane reveals himself to be not quite dead, flips out, and orders GDI nuked.
This occurs in Kingdom Hearts II when Maleficent teams up with Sora against Organization XIII.
Interestingly, you never really see Maleficent and Pete helping, just getting ready in a Bolivian Army Ending kind of way. Sora mentions that they've found something worth fighting for, and then we never see them again. Things are back to normal as of Coded though.
Super Robot Wars Destiny is an interesting example. While the game includes antagonists from Gundam ZZ, Char's Counterattack, and Gundam Wing, the situation at hand causes them to have the competence to ally with you all at the start since things are bad enough. Due to the Zanscare Empire attacking Earth, along with the Invaders, and the Protodevlin, and the united alien forces of the villains from Daltanius, Godmars, and Grendizer, your heroes quickly realize the only organizations out there that still have the sheer manpower to defend humanity are the Principality of Zeon and the Order of the Zodiac. Roger Smith takes care of the negotiations. This results in the first heroic roles for longstanding villains like Haman Karn and Treize Kushinada.
Super Robot Wars likes to play with this in smaller ways as well. For instance, Super Robot Wars W has a stage where Tekkaman Evil is forced to (briefly) work with the heroes because of the takeover of Tokyo by the Zonder. On the Selena route of Super Robot Wars Alpha 3, not only does Selena herself spend some time assisting the Cruscet team, Andrew Waltfeld and his adjutant Martin Dacosta assist the Alpha Numbers in holding off an attack by the Barota in a later stage.
One OG example is when Sanger and Elzam storm the Tesla Liecht Institute to retrieve the Dynamic General Guardians being kept there from the Inspectors. When Sanger's Grungust Type-3 gets damaged, the Inspector Vigagi is about to land a fatal blow when Wodan Ymir appears and intervenes, claiming that he is the only one allowed to kill Sanger. Wodan buys enough time for Sanger to activate the Dygenguard, and goes so far as to be the one who helps Sanger retrieve his Type-3 Zankantou (a job that was given to Elzam in Alpha 2) to continue fighting when Dygenguard's original weapons malfunction.
In the final episode of The Inspector anime, Kyosuke and Axel end up working together to take down the Big Bad.
Super Robot Wars EX is an interesting case because some of the characters you can recruit ARE enemies in their respective series that are cooperating because they are stuck in La Gias with no way back. Shu's route is unique because the only heroes you actually can recruit (on that route) are the GoShogun team and Quattro. The rest are all villains like Todd Guiness and Jerid Messa.
Spider-Man: Friend or Foe has the entire premise of its story built around this trope. The story involves several prominent members of Spider-Man's Rogues Gallery being mind controlled by another villain. Spider-Man subsequently confronts the mind controlled villains and frees them from the mind control, at which point they readily agree to join forces with Spider-Man to find, and exact their revenge upon, the one who was mind controlling them.
In Spider-Man: Web of Shadows, Spider-Man decides to break the evil mad scientist known as the Tinkerer out of Ryker's Island to get him to build a device capable of decimating Venom's symbiote army... if only because Reed Richards Is Useless by being absent when he tried to phone him, Tony Stark and Hank McCoy are also absent, and he doesn't feel like dealing with Hank Pym. The mission where you do so also involves another Enemy Mine —- namely, freeing the Rhino and riding him to break through the island prison's walls. Some time later, when the Tinkerer requests that he be transferred over to the Kingpin's facilities to complete the device, Spidey and SHIELD end up forming one with the crime boss as well.
Notable in that Spider-Man fully acknowledges that breaking out the Tinkerer is a bad idea, and he doesn't like it (unless you're playing the evil path), but that the threat of the symbiote army is so great that he really can't wait for anyone else to show up and help him solve the problem. This and other questionable actions get him in a lot of trouble when Wolverine shows up and calls him out.
There's also the possibility for a third, very temporary Enemy Mine. In order to get to Ryker's you have to make one of the "good or bad" choices that are sprinkled throughout the game. Choosing the bad option has you get a ride there from the Vulture. (In case you're wondering the good option is a ride from Moon Knight.)
In the DS version, you can also choose the Dark path by helping the Green Goblin.
Mana Khemia: Alchemists of Al-Revis: Hilariously played with; the True Companions go into the depths of a monster-infested dungeon, trying to find the cure for an ailing friend, and found themselves mobbed by monsters. Then comes the game's Goldfish Poop Gang (doubtful of the status as real enemies). They think they're going to cause trouble again, only to find that the latter group, under orders, is there to help them. Made even funnier by the following dialogs. During their arrival:
"Not now..." "We don't have time to play with you!"
The second dialogue is that after they reveal their plans, and persuade the heroes to make their escape with the medicine
Renee: ...Umm, maybe you shoulda been honest and let them help. Tony: Don't be stupid! Coming to their rescue to ask for help? That's just uncool.
In The World Ends with You, at one point, Neku and his partner see two Jerk Ass Reapers getting attacked by Taboo Noise. At this point you have the choice of helping the Reapers or letting them fight it off on their own. Hilariously, if you choose to help, Neku justifies it by saying it'll really annoy them, since Reapers are supposed to be killing Players, not being helped by them, and if you choose to leave them to their fate, Neku justifies by saying, "Just for you, Jerk face!"
Subverted in the DS version of Mario and Sonic at the Olympic Games. When Toad mistakes Omega as one of Eggman's loyal robots, Omega states that Dr. Eggman is in fact his enemy. Toad questions Omega on his blockade using this trope's logic, only for Omega to simply respond with "Unverified" and restate his threat to the team. As you can guess, he does not end up assisting the team, instead preferring to take on Eggman himself. It comes as a surprise to Toad.
In Sonic Lost World, Sonic causes Eggman to lose control of the Deadly Six, who immediately turn on the doctor. This proves out to have been a bad move on Sonic's part, as the Six immediately start misusing Eggman's energy-sucking machine to suck out all life from Sonic's world. Eggman, wanting to conquer the world and not destroy it, teams up with Sonic until the Six are put out of commission. However, he fakes his death just before the job is finished, and tries to kill Sonic the instant the last of the Six are defeated, arbitrarily becoming the final boss despite not being the primary antagonist for the majority of the story.
In the intro to Mortal Kombat Deception, Raiden, Shang Tsung, and Quan Chi attempt to fight that game's Big Bad, the Dragon King Onaga. Unfortunately, when Raiden realizes that they aren't doing any damage... he causes an explosion that appears to kill himself and the sorcerers while obliterating the palace they were in. And Onaga was unscathed.
Kratos after his betrayal, when you invade Forcystus' human ranch
X-Men Legends II had the X-Men and their old enemies the Brotherhood teaming up to fight the forces of Apocalypse, who had abducted members of both teams.
Some are happier about it than others. Scarlet Witch and Toad get along great with the X-Men and become quite friendly, while Magneto simply tolerates them, and Sabretooth and Juggernaut are constantly taking verbal potshots at the X-Men all game.
The original game also has a brief moment of this. The first time Magneto confronts the X-Men, the entire mansion gets attacked by an army of sentinels, causing the X-Men and Magneto's forces to fight alongside each other against the mutant-hunting robots.
In Thief: The Dark Project, there's actually a mission named Strange Bedfellows, in which the main character agrees to help the Knight Templar Hammerite faction in exchange for their help against the Pagan Big Bad. In Thief II: The Metal Age, the main character teams up with the survivors of the Pagans against a Hammerite splinter group. In Thief: Deadly Shadows, it's possible to ally with both the Pagans and Hammerites if you get your reputation with both groups high enough. they'll even help you out in the insane Finale after the Big Bad declares war on the city. Granted, they (and everyone else in the city) will fight the Big Bad's creatures even if you didn't ally with them earlier, but unless you ally with them they'll also attack you as well.
A mission in Fire Emblem Awakening has your group picking a side between two rival mercenary factions. If you refuse to pick a side, they both gang up on you.
In Phoenix Wright: Ace Attorney, the fifth case practically loses the prosecution as both Phoenix and Edgeworth fight to reveal the true killer, Damon Gant.
Then in Justice For All a similar arrangement is made where both Phoenix and Edgeworth attempt to prolong the trial as long as possible in order so the police might discover where the kidnapped Maya has been brought.
In Trials and Tribulations, Edgeworth actually takes over the defense for the case since Phoenix was stupid enough to run across a burning bridge a hundred feet over a freezing river and is incapacitated. To make it even more interesting, he gets Franziska to serve as the prosecution, as she's the only one who wouldn't point out to the (new) judge that Edgeworth is actually a prosecutor and not a defense attorney.
Halfway through Advance Wars: Days of Ruin (after Captain Brenner is killed), Tasha, Gage and the surviving Lazurians temporarily set aside their differences with Will and the 12th Battalion to help him stop Admiral Greyfield's New Rubinelle Army from launching missile strikes against them.
At the end of Bomberman 64, halfway through the final battle against Sirius — the Magnificent Bastard who used the hero throughout most of the game — Regulus, who was presumed dead earlier appears and saves Bomberman's life at the last second. After some dialogue, Regulus forms a temporary alliance with Bomberman to take down Sirius. He even helps Bomberman escape the collapsing fortress before reminding him that they aren't friends and they will fight again.
Shirou and Kotomine in Heavens Feel route of Fate/stay night. They're both very clear on the fact that they're doing it for entirely different reasons and that after cooperating, they're enemies again. Still, it leads Shirou to realize that he actually likesKotomine and that's why he avoids him. They're not actually that different apart from the whole, you know, evil for the fun of it factor.
And in Unlimited Blade Works, Lancer joins forces with Shirou and Rin against Caster and Archer on the orders of his master, which would be Kotomine again. He even sticks around to save Rin from Archer just because he feels like it afterwards, despite technically being their enemy.
The entire mechanics of the Holy Grail War encourage/force the Masters to get into such scenarios, since with seven factions battling each other, there will always somebody trying to score a kill while two others are fighting or an enemy one can't beat alone. Technically, Shirou's and Rin's alliance started out this way, but they never got to duke it out in the end.
In Fate/Zero, there also was such a scenario against Servant Caster. Such servant and his Master, Ryuunosuke Uryuu, were brutal Serial Killers and their favorite preys were children, so the whole Grail War was temporarily put on hold solely to get them taken down. That's how bad the situation was. Ultimately, Ryuunosuke is sniped down by Kiritsugu, and after this Caster and a monster he had summoned are defeated by Saber, but only with the assistance of Rider and Lancer.
In one of the path branches in Devil Survivor, Midori teams up with Kaido to keep Keisuke from pulling a Karma Houdini and getting away with his Knight Templar stint without a fight. She does so hoping she can restrain Kaido from killing him, but wonders about her ability to do so a tad too late.
The freeware game Sonny has the titular character and Veradux to team up with Galiant, an elite soldier of Zombie Pest Control Inc., by pretending they're also ZPCI soldiers, to fight the super-powerful zombie Baron Brixius. Once that's done, however, Sonny and Veradux decide to take Galiant out before he finds out they're actually zombies too, and he thus becomes the game's Final Boss.
Baten Kaitos has Aimee and Folon helping the main party to infiltrate the The Very Definite Final Dungeon despite having fought the group multiple times over the course of the game.
Captain Price:Makarov, you ever heard the old saying "the enemy of my enemy is my friend"? Vladimir Makarov: Price, one day you're going to find that cuts both ways.
In The Godfather: The Game, in the cutscene of Sonny's death you can clearly see mobsters from the Tattaglia, Stracci and Cuneo families working together against the victim.
Overlord II has the Evil Overlord offered an alliance by the Big Good Queen Fay, ruler of Light Magic to take down the magic-destroyingGlorious Empire. She helps by reconstructing the Tower Heart of the first game and sacrifices her temples to power it up. When that proves to be insufficient, she decides that she'll have to sacrifice her own magical energy and allows the Overlord to drain her. However due to his evil influence seeping through her body she is eventually driven insane, becoming the Fallen Hero Dark Fay who joins the Overlord as his mistress.
Ssssssort of. Queen Fay turns into Dark Fay from being exposed to too much of your Evil Presence spell (Force Lightning and a Jedi Mind Trick in one.) This leads to Corruption... Unless you decide to "overcharge" her and explode her, for Destruction points. She still joins you, only this time she's a spirit. The real kicker? Dark Fay is more explicitly evil and violent, while Ghost Fay is more innocent and aloof. Corruption gets you a Woobie, Destroyer of Worlds, Destruction gets you an artistic, aethereal sidekick.
Crash Twinsanity makes this into a game feature by making Dr. Cortex a total Butt Monkey. Crash and Cortex being forced to work together usually means whacking enemies with Cortex, tossing Cortex over a gap for him to do something, clearing his path while he runs in a screaming panic, using him as a snowboard, or controlling the two as a Big Ball of Violence when Cortex decides to beat up Crash.
You really have no choice as he's forced to join your group temporarily anyway as part of a larger enemy mine situation with the two warring kingdoms vs the invading aliens. Afterwards the war is resolved peacefully. The only optional part is whether you choose to have Albel join you for the rest of the game, or send him back to the army that loaned him to you.
He only turns up to join permanently if you go through a private action with him earlier and tell him you're not his enemy. He genuinely doesn't want to be your enemy, regardless of common threats.
Mass Effect 2 has Commander Shepard brought back to life by The Illusive Man, who may have been responsible for killing his/her squad in the Sole Survivor backstory, in order to combat the mechanicalEldritch Abominations out to destroy humanity (and all galactic civilization, but Mr. Illusive doesn't really care about them), even willing to recruit notably Badass aliens. Particularly relevant if Shepard is played as Paragon, who does not hesitate to tell TIM that he/she's barely tolerant of his organization only because no one else will help him/her and in the end can deny him the Collector Base and technology to "secure human dominance".
The 2nd game even features a villainous example: the vigilante Archangel does such a good job of ruining the collective days of Blue Suns, Eclipse, and the Blood Pack mercenary gangs that they all team up to take him down, despite usually being at each other's throats.
Mass Effect runs on this trope anyway. You gather a team of people from various species, and almost all of them are at least a bit prejudiced against the other races due to past events such as the First Contact War and the krogan genophage. They all end up working together to save the universe from a common threat. One of those people you can recruit is Morinth, Samara's sociopathic daughter, who intended to add Shepard to her long list of Death by Sex victims.
The geth and the Reapers do this in 3. Having declined an alliance with the "Old Machines" once before, the geth are forced to reconsider after the quarians try to wipe them out for the second time in three centuries. Faced with creators who seemingly refuse to treat them as equals and no help from any other organics, they decide that giving up their free will is preferable to being exterminated. It takes the combined efforts of Shepard, Legion, Tali and Zaal'Koris to get both species out of that mess intact.
The entire Galaxy unites because of this in 3. Most of the various forces bitterly hate each other but can be convinced to fight side-by-side, including the Turians and Krogans, the Quarians and the Geth, the Humans and Batarians etc. The Rachni, once the bane of the Galaxy, also can become allied forces due to their debt to Shepard. The Godzilla Threshold has a way of making everyone come together.
The batarians are especially interesting, because if you played the "Bring Down the Sky" DLC for the first game and let the Big Bad escape, Balak returns in 3 and, due to a severe case of You Are in Command Nowmore The Batarian Hegemony was directly on top of the Reapers' point of arrival into the galaxy, and their higher-ups were already indoctrinated due to contact with a dead Reaper they'd found., is now the highest-ranking batarian naval officer left alive. You can kill him, or, despite him having a gun to the back of your head, browbeat him into adding his forces to the war effort. Afterwards a C-Sec officer asks if Shep wants to have him arrested.
Shepard: I want you to put a bullet in his head. But we're all making sacrifices today.
In the Leviathan DLC, Shepard manages to broker an alliance with the race the pre-dated the Reapers. However, the Leviathans make it very clear that the only reason they are helping is because they see the Reapers as having stolen the Galaxy from them and, since they consider themselves to be God-like, are rather pissed off that the Reapers never paid proper "tribute" to them.
In the Omega DLC, Aria T'Loak recruits Shepard to help her retake Omega. After her initial plan of attack fails, she's forced to enlist many of the gangs that formerly opposed her, (including one lead by a former lover), in order to form a rebel army capable of driving Cerberus from the station.
This is the best way to describe the relationship between Kane and Lynch. They consistently hate each other throughout the game since Lynch was originally a thug hired by The Syndicate to watch Kane. Hilarity Ensues as Lynch's Ax-Crazy nature gets the better of him...
In Prototype, Blackwatch works with Alex Mercer to defend the Bloodtox Pump from the Infected, and there are also side-events scattered around the city that involve fighting with the Marines or Blackwatch to beat the Infected. However, other than these few exceptions, Mercer and the Military are mortal enemies.
In Freespace, the Terran-Vasudan War comes to an abrupt halt with the appearance of the Shivans, who are trying to kill both of them. Since the Shivans are more than capable of wiping out both species, the two agree to a cease-fire to deal with the common threat. The cease-fire holds and eventually becomes the foundation for an alliance between the two species.
In the fan-made Blue Planet expansion, events transpire such that both the Terran forces of the GTVA and the UEF respond to a Vasudan ship in distress. The captains of both ships agree to set aside the war for the moment to rescue the Vasudans, and the deployed fighters make small talk with their opposite numbers. It all falls apart when a second UEF ship arrives and, not knowing of the cease-fire, obliterates the GTVA ship. The UEF commanders were furious, since it made them look very, very bad in front of the Vasudans, with whom they had hoped to win political favor.
In F.E.A.R. 3, Paxton teams up with the ex-FEAR commando Point Man.
Snake can form this with the non-P.M.C. forces in Metal Gear Solid 4: Guns of the Patriots. Normally they see you as a threat and shoot on sight, but if you take care not to return fire and only shoot Liquid's forces, they'll become friendly. They'll even go as far as to cover you and give you items.
Raikov's recruitment in Metal Gear Solid: Portable Ops was mostly due to this trope, as he seemed to hate Gene enough to even ally himself with Naked Snake mostly to get revenge on Gene for humiliating him and locking him up (In case why it is worded this way, its because he has a lot of hate towards Naked Snake because he was involved with the death of his lover, Colonel Volgin, in Metal Gear Solid 3: Snake Eater.) Roy Campbell even lampshades this by quoting the adage "The Enemy's Enemy is my Friend" during both the mission briefing and the radio call at the start of the mission.
The whole point of the Warriors Orochi games; all of the characters contained within are from either the Three Kingdoms period of China's history or the Warring States period of Japan's, and many of the characters are sworn enemies. However, a few of the Dream Mode stages in Warriors Orochi 2specifically invoke this trope by teaming up characters who normally hate each other, such as the stage where Dynasty Warriors Guan Yu, Xiahou Dun, and Lu Meng team up to rescue Liu Chan from Samurai Warrior character Hideyoshi Toyotomi.
In Dragon Age: Origins, after punching some sense into Loghain's thick skull and overthrowing him from the throne, you can choose to spare him from execution and instead conscript him to the Wardens as a chance of redemption. He will then join your party and help you fight the Blight at the cost of Alistair, who will be so outraged with the decision of pardoning Loghain that he will leave.
Also shows up in the myriad groups you are assigned to recruit; though nowhere so much as the Dalish working alongside humans.
Even the Warden can be played like this with the Dalish and Dwarven backgrounds, not interested in ending the Blight so much for Ferelden's sake, but to prevent it from spreading and affecting their people.
Loghain: Pray our King is admenable to reason.
Dalish Warden / Dwarf Warden: The Dalish have no Kings! / He's not my King!
Can happen in Dragon Age II, depending on your choices and who you side with in the end. No matter how you feel about the mage/templar conflict, many people will probably side with the mages just to piss Meredith off. Also, this is Fenris' opinion on fighting alongside mages, particularly Merrill, with the implication that he won't straight-up gut them because of loyalty to Hawke. The unique buff you get for a Rival Fenris is "Enemy of my Enemy".
In the Mark of the Assassins DLC, Tallis is revealed to be working for the Qunari, who are feared by the rest of Ferelden. This quickly earns her the scorn of most party members since they're technically now working to save a group that most of them despises.
Similarly, if you choose to side with the mages in the final confrontation and coerce Fenris/Aveline into joining you, or vice versa with the Templars and Merrill/Anders. The first three are possible with Friendship or Rivalry, but it specifically takes a maxed-out rivalry meter for Anders to swap sides.
Explicity stated to be the relationship between Mage!Hawke and Knight-Commander Meredith. She only lets Hawke continue to roam free because it's more useful to turn their magic against Kirkwall's enemies. That, and, she's utterly terrified of them!
When you enter Polito's office, SHODAN tells you that the reason she wants you to get rid of the Many is because they turned against her after the Hacker sabotaged her on Citadel Station. The Many grew up without her tutelage, and they decided that they hated the mechanical ways of SHODAN and wanted all of the universe to be covered in their organic ways.
AdventureQuest Worlds has King Alteon and Gravelyn, Sepulchure's daughter, into forming a Great Truce between Good and Evil to deal with the threat of Drakath and his forces of Chaos, including the 13 Lords of Chaos.
In Bet On Soldier, you spend most of the game fighting through the Bet On Soldier tournament in order to confront the BOS World Champion, Igor Boryenka, who you believe to be responsible for the murder of your wife. Once you finally defeat Boryenka, the real Big Bad punishes you both by forcing the two of you to fight together in an Arena deathmatch against wave after wave of the best fighters in the BOS League. It's actually a pretty cool level, since Boryenka retains his boss-like health and damage output, but the sheer number and skill of opponents the two of you face make it seemingly impossible for him to survive to the end.
In Fallout: New Vegas, if you take the NCR, Mr. House or Independent path and complete sidequests pertaining to said factions, it's possible to have the NCR, Brotherhood of Steel, Great Khans and Enclave Remnants fighting together against Caesar's Legion in the final battle for Hoover Dam. All of these groups have been mortal enemies of the NCR throughout history, with the Enclave having been the Big Bad of the previous two games.
Near the end of Crysis 2, the remaining members of the CELL PMC that has spent the entire game trying to kill you end up teaming up with you against the Ceph alien invasion, because their dying boss makes it clear to them that their entire chain of command is now dead and you are now humanity's last hope for stopping the aliens.
In the Sundown Kid's chapter in Live A Live, Sundown Kid is being relentlessly pursued by the bounty hunter Mad Dog. They put their duel on hold when the town they stopped at is attacked by Odie's gang of outlaws. After working together to defeat Odie, Mad Dog will immediately try to settle things with Sundown once and for all, to the strong protests of the townspeople they just saved. Sundown can either finish off Mad Dog or spare him to fight another day.
In the remake of The Tower of Druaga for the PC Engine, Gilgamesh, instead of killing the Succubus, must convince her to help him so he can get the Blue Crystal Rod and defeat Druaga.
One mission in Perfect Dark sees protagonist Joanna Dark, captured by Skedar in the mission beforehand, locked in the same cell as the head of the very organisation the game squares you up against, Cassandra de Vries. She willingly gives her life to allow Joanna to escape.
In the Skyrim quest Cure For Madness, you have to hunt down Cicero after he apparently turns rogue and attacks Astrid. However, you can choose to spare his life, and later he will act as a follower for you. Similarly you can play as an Imperial, High Elf, Dark Elf, etc whilst working for the Stormcloaks (who are known for the xenophobia of some members).
In Kid Icarus: Uprising, immediately after a Męlée ŕ Trois between Pit, Viridi's Forces of Nature, and Hades's Underworld forces, the fight is put on hold to deal with an alien invasion out of nowhere. Though Hades still can't resist dropping a Chest Monster in Pit's path at every opportunity, Viridi takes to the team-up very well, and remains a tenuous ally for the rest of the game.
Later, Medusa appears during the final battle to sock Hades in the face before he can finish Pit off, having been revived by the lord of the underworld, but pledging that she would no longer be his puppet. She's killed for her trouble, but it gives Pit, Viridi, and Palutena the opportunity they need to finish Hades.
The penultimate mission in Nexus: The Jupiter Incident, in which you have to fight waves of entire fleets of enemies, has the possiblity of you getting reinforcements in the face of a Gorg warship captained by Chief Zatuk, the Gorg ruler. Slight subversion in that Zatuk never wanted to fight humans or the Vardrag, but the Gorg society is heavily clan-based, and it's several powerful clans who wish to fight.
Half-Life - HECU and Black Ops are both there to kill Freeman and fight against each other.
In episode 303 of Sam & Max: Freelance Police, Sam is trying to sneak in and retrieve Max's brain from a room where General Skun-Ka'pe and Monsieur Papierwaite are busy firing guns and slinging spells at each other. Unfortunately, Max notices him...
Max: Sam! Get me outta here! This whole place smells like gorilla and patchouli!
Skun-Ka'pe:(turns, slowly) Sam? The interloper who foiled my scheme to collect the toys of power and re-imprisoned me in the Penal Zone?!
Papierwaite:(turns, slowly) Sam? The great-grandson of the poltroon who put the kibosh on my intricate plan to unleash Yog-Soggoth and take over the world?!
Skun-Ka'pe: I hate that guy.
Papierwaite: I hate that guy!
In Warhammer 40,000: Rites of War, you, playing as the Eldar, spend the first half of the campaign fighting your way through Imperial forces, including PDF and Guard forces, Sisters of Battle, and Space Marines. Just when you finally break the back of Imperial resistance on the planet, you find out that the Tyranids are attacking, and that there is a Tyranid hive fleet approaching. All of a sudden, you are teaming up with The Remnant of Imperial forces to fight the Tyranids, meaning you can recruit Guard, Sororitas, and Space Marine units into your army. Unfortunately for the Eldar, they're still going to have to bear the brunt of the fighting, even though, in the fluff, the Eldar would prefer to have the humans do the heavy lifting.
In the second game, Dmitri Lousteau initially helps the Coopers rescue Murray in exchange for being released from prison. Since he's not exactly that evil to begin with, he eventually pulls a full Heel-Face Turn and joins the Cooper Gang full-time.
In the third game, Panda King begrudgingly joins the Cooper Gang in exchange for their help to rescue his daughter.
In Project X Zone there are several examples most of them being solo units.
Saya joins your team in Chapter 26 because the only reason she joined forces with Oros Phlox was because she needed their help to finish Byakuya X, after that she immediately ditches them, that and they were planning to use it for something other then it was intended for.
Juri joins your team in Chapter 27 after she finds out Seth was planning to kill her and take back the Feng-Shui Engine in her eye. Chun-Li manages to convince her to fight with them because the alternative was fighing against your group.
T-elos is the only example of a character that's part of a pair unit. She teams up with KOS-MOS in Chapter 19 after Seth was planning to kill her to take her machinery for himself. T-elos stops him because she wants to be the one to do it. KOS-MOS convinces her to help the group because it's a really bad idea to fight with the Dimensional Barriers crumbling, and to have their showdown on their own world where it will stick.
One mission of the SNES Front Mission had your unit protecting Sakata Industry's CEO from terrorists, and Lloyd's Arch-Nemesis Driscoll swings by to help you out because he needs Sakata alive as well. Needless to say he's a complete Crutch Character.
Early on in Metro Last Light, Artyom is captured by the Reich and sent to a prison facility, where he ends up working with Pavel, an imprisoned soldier of the Red Line, to engineer an escape. Pavel and Artyom both lampshade this:
Pavel: So...um... you're with the Spartan Order? I'm from the Red Line. Our superiors are not on the best of terms, eh? But I say fuck that- uh, fuck that! The grunts stick together, uh?
Artyom: My escape from the Nazi prison could be entitled "The enemy of my Enemy is my friend"... I never liked communists much, but Pavel acted like a real hero.
In Dracula: Love Kills Dracula and Van Helsing teamed up to stop the Vampire Queen from conquering the world.
In the first part of Witches' Legacy 3: Hunter and the Hunted the first game's Big Bad Elizabeth teamed up with the main character in order to rescue the latter's adopted daughter from the Order of Witch Hunters, at least until Elizabeth got the main character captured, possessed the daughter and tried to open a portal to the spirit realm.
Seems almost guaranteed to happen at least once per game in the Suikoden series, with quite a few instances of your enemies becoming official members (and temporary allies) of your own army. Also happens between individual army members, some examples being Ayame and Watari in III, Klaus and Kiba in II, and Nakula alongside Shigure, Sagiri, and Oboro in V.
Breath of Fire IV finds Ursula and Scias teaming up with you, despite being (separately) employed by different enemies of yours (Ursula is from the Fou Empire; Scias was employed by Ludia, whose relations with the heroes are... shaky at best).
Clive Barker's Undying: The skeletons in the monastery aren't actually controlled by Lizbeth, according to Word of God. That doesn't stop them from temporarily allying with Lizbeth and her Howlers to try to kill you.
Guild Wars Eye of the North has a truce between the rebellious Charr and the Ebon Vanguard, ordinarily fierce enemies, in order to overthrow the current Charr leaders and stop the Destroyers.
Guild Wars 2 has the Charr and humans reluctantly putting aside over one thousand years of hatred and three centuries of near-constant warfare in order to fight against the Elder Dragons.