Crash Twinsanity has it when Crash and Cortex team up to fight the Evil Twins. For starters, there's the game's Rollerbrawl mechanic, as well as the fact that Crash also tends to use Cortex as a bludgeoning and throwing weapon. The game's tagline even lampshades it ("They're working together, but they don't have to like it!").
Mega Man and Proto Man: They never actually have a problem working together, but they also never actually work together. Proto Man does his own thing while Mega Man saves the day (usually). They help each other out, however.
Mega Man and Bass, though again, they never work together, just towards the same goal.
Knights of the Old Republic II: The Sith Lords, big time. Being a Ragtag Bunch of Misfits the Exile's companions have only their mutual loyalty to him/her in common, and nothing else. Being hostile to each other because of their directly conflicting views and opinions. Bao'dur hates Mandalore for what his people did during the war. Handmaiden sees Visas Marr as a rival for the Exile's affection. If the Exile is female then Atton dislikes Disciple for the same reason. None of the droids are particularly fond of each other. Hanharr hates everyone, and nobody likes Kreia. Mira being pretty much the only one who doesn't have it out for anybody else.
If you count the restored content, by the end of the game almost everyone is trying to kill each other for one reason or another.
Alistair and Morrigan of Dragon Age: Origins. Big time. Especially if they sleep together in a dark magic ritual to save his/the PC's life.
This theme continues on into Dragon Age II as well; Fenris and Anders aside from their deep hatred for each other despite an awful lot of similarities tend to alienate others. Fenris in general dislikes mages (though he has less of a problem with the Hawkes) and Anders' obsession with the Mage/Templar conflict compounded by Vengeance leaves him antagonistic towards most of the party members by the third act.
Depending on whether Hawke sides with the mages or Templars in the endgame, certain teammates with full Rivalry scores, but opposing alliances, can be convinced to continue working with Hawke for the final boss fights.
In Dragon Age: Inquisition, Vivienne tends to look down on almost every other character due to her classism and snobby demeanor. As a Pro-Circle mage with a lot of political influence, she tends to treat most characters with disdain, particularly those with differing opinions of mage politics such as Solas or those from lower-class backgrounds such as Sera and Blackwall. Cole, in particular, gets the scorn of both Vivienne and Sera due to his status as a spirit in the form of a human and both of them refer to him as "it".
While Hawke gets along fine with their Grey Warden friend at first in Inquisition, the revelations as to what the Grey Wardens have done and are doing infuriates Hawke leading to a back and forth What the Hell, Hero? between the two of them, with the Warden responding by calling out Hawke's part in the beginning of the Mage-Templar War. Alistair in particular takes his/her anger at the Wardens quite personally.
Bowser, in Super Paper Mario. Mario's archenemy first refuses to join Mario in his quest to stop Count Bleck from wiping out all dimensions, even at the first request of Peach (despite the fact he finally got one of his dearest wishes come true thanks to the Count who forcefully married them). He changes his mind however, very begrudgingly, once Mario and Peach point out that his desire to be the ruler of the world would never come true should their world be destroyed by the Count; and his minions are now brainwashed to serve the Count, infuriating Bowser at the idea.
Mass Effect 2. Similar to the Knights example above, several of your team-mates go at it against each other with biotics (Jack and Miranda) or end up with weapons drawn (Legion and Tali) forcing you to pick sides (or choose a third option if you're charming/intimidating enough). And of course, there's the Justicar who agrees to work with you but also vows to kill you after the mission if you're too much of a Renegade.
In the first game, Garrus and Shepard can have this dynamic if one plays Shepard as a Paragon. Garrus wants Saren, and the antagonist of his personal mission, dead, with very good reason. He really doesn't care to deal with any red tape or rules in pursuit of these goals, which is mostly why he left C-Sec in the first place. Paragon Shepard can insist on playing everything by the book because the rules are there for a reason. This can continue to the point that Garrus grumbles it's like he's still in C-Sec. Eventually, they get past it and he becomes one of Shepard's most loyal and closest friends.
Also in the first game, depending on how Wrex is talked down on Virmire, him agreeing to help you destroy Saren's facility follows this. Turned around in the third game, if Shepherd would rather not cure the Genophage. If you don't cure the genophage, Teeth-Clenched Teamwork turns into a shootout on the Citadel.
Overall, this is something of a theme for Shepard and Cerberus. They tried to kill Shepard in the first game and s/he ruined several operations, but now they're working for a common goal. By the end of the trilogy, they're back to the first game relationship, only with more personal hatred and heavier artillery on both sides.
Miranda is initially distrustful of Shepard, particularly Paragon who is extremely opposed to Cerberus, not trusting them to truly work for the better of Cerberus. Once Shepard helps her protect her sister with no ulterior motives, Miranda greatly warms up to him/her, culminating in her abandoning Cerberus in favor of Shepard and a friendship that lasts into 3.
In Mass Effect 3 much of the galaxy is in this position in their rather desperate fight against the Reapers. Depending on Shepard's actions the final united force can include krogan and turian armies fighting together on Palavan, the Geth and quarians fighting together over Earth and the rachni helping build the crucible.
One of the people that Shepard can recruit is the batarian terrorist, Balak, who Shepard stopped from making a Colony Drop on a human colony three years before. Despite now being on the same side, both Balak and Shepard make it clear how much they despise each other.
Officer Noles: Do you want me to arrest him? Shepard: I want you to put a bullet in his head, but we're all making some sacrifices today.
Mass Effect: Andromeda: Liam and Vetra, thanks to Liam, who has a habit of irritating his teammates at the best of times, being incredibly rude and hostile to Vetra on account of Anger Born of Worry. While he does apologise for what he says, both of them admit that if and when everything's over, they're going to live very far away from one another.
The team of Sonic and Knuckles in Sonic Advance 3. When the two are chosen in the character selection, the two are noticeably uncomfortable about it. Eggman actually teams up with Super Sonic to fight the True Final Boss in this game, however he averts this trope. His only line of dialogue is him telling Super Sonic to use tag action to hurt the boss.
One of the verses of Knuckles' theme song in Sonic Adventure actually points out about how he views teamwork:
I have no such things as weak spots Don't approve of him, but you gotta trust him This alliance has a purpose This partnership is only temporary.
Also, Shadow and E-123 Omega in the beginning of the Team Dark Story in Sonic Heroes after Rouge stopped them from fighting each other. They've got better from then on.
Knuckles and Rouge in Sonic Rivals 2. Justified since Knuckles can't trust her in retrieving the Master Emerald from Dr. Eggman with him.
Sonic, Tails, and Eggman develop this in Sonic Lost World. They spend just as much, if not even more, time bickering with and insulting one another as they do actually working together.
In Scaler, the first person the titular character meets is a Lizard Man named Leon. While he's no less hostile than any of the other wildlife Scaler's encountered so far, he and Scaler are united in their mutual hatred of the Big Bad, Looger. They form an uneasy partnership to try and deal with him. They eventually grow to get along, though they aren't willing to admit it at first—until they realize they're long-separated father and son.
Kane & Lynch. In the first half, they are actually forced to work together, much to the disdain of both- in the second half, they're working together to kill a common enemy, but they still hate each other. In the sequel, they both end up pissing off a major crime lord in China, once again forced to work together to survive.
A few of the characters you get in Baldur's Gate II: Shadows of Amn often argue amongst themselves and occasionally leave the party due to the other character. Example: If you keep Keldorn the paladin and Viconia the dark elf in the party together for too long, Keldorn will pick a fight with her for the sole reason of her being a dark elf (though given how he reacts to a certain renowned good dark elf he might have been able to look past that if it wasn't for his other issues with her).
The Australian team in World Destruction League: War Jetz fight among themselves as much as they attack the player. Good thing too, as they fly the best plane in the game.
Master Chief John-117 and Arbiter Thel 'Vadam start off like in Halo 3, given that they were on opposite sides less than a month ago. They end up becoming something of Bash Brothers by the end, though.
Final Fantasy XIII starts off like this; after being turned into l'Cie they are forced to cooperate in order to survive, but each member of the team has it's own goals and many members hate other members. This often leads to the party being divided into smaller groups and many fights between main characters. Other than Hope holding a large grudge that borders on hatred toward Snow, Sazh could only barely keep himself from killing Vanille, Lightning really doesn't like Snow to the point of punching him three times, and tries to leave the entire party behind on several occasions and doesn't hold back on punishing Fang for her part in getting them in this mess either.
The team in the Fallout: New Vegas DLC Dead Money composes of a band of individuals with their own emotional baggage (and you) who are forced to cooperate together due to the fact that their lives are under the whims of an even worse lunatic who's strapped Explosive Collars on all of them and linking them to ensure cooperation. The Courier is forced to work with them to progress, all the while trying to ensure each others' survival. Later on, when the team finally splits up, you're given the option of either killing them or helping them deal with their own issues, after which they might try to help you in the final mission. At the end, if everyone survives long enough to deal with their employer and remove the threat of their collars going off, they still don't trust each other, but decide to part ways peacefully.
The Alliance and Horde forces guarding the Dark Portal (the common entrance into Outland for both factions) in the Blasted Lands are forced to put aside their hatred for one another for a common cause, but neither is happy about it, and you will be asked to spy on the other faction's plans.
And then there's pick up groups for the players, which range from being decent enough to clear the dungeons to being plagued by bickering, infighting and scapegoating for failures, and being unable to make any progress. To be fair, guilds are also susceptible to drama that can result in players making an exodus from the guild or the entire guild breaking up, despite (or because) of the fact that the players tend to group with each other more often and are used to how they work as a team.
The issues associated with pick up groups are only escalated by the pick-up raid feature introduced in Cataclysm. Take all the problematic combinations you can get with jerks, incompetents, and trolls in a five-man group, and multiply that by five. All new avenues of conflict open up when you realize that healers and tanks, while previously unique and indispensable to their teams, are now in competition with each other.
The Ashen Verdict is a combined order of Paladins and Death Knights devoted to fighting the Lich King. The former, being more traditionally heroic, and the latter, being a group of anti-heroes, often clash over tactics, such as whether to fire on enemy forces with a risk of harming soldiers webbed as human shields. Unlike the Alliance and the Horde, however, they can actually work together.
In Cataclysm, when players are sent to meet Thrall at the Maelstrom, the Alliance quest giver knows full well that an Alliance hero would feel this while working for the former Horde warchief. Unfortunately the developers forgot this and as the expansion put more focus on Thrall, they were faced with angry Alliance players playing patsy to a character that was their enemy just prior to Deathwing's return.
In the Legion expansion's Warlock class quests, human warlock Kira Iresoul is initially unwilling to work with you because of your association with her former mentor, orc warlock Ritssyn Flamescowl. After you do some quests on her behalf, she agrees to out of obligation to you, but regularly insults or threatens Ritssyn.
Also from Legion, the high, night and blood elves ally with the Nightfallen rebels against the Nightborne. Unfortunately, the three groups of elves have long-standing grudges against one another, which one NPC says are enough to make the enmity between the Alliance and the Horde look petty, and Tyrande, leader of the night elves, doesn't fully trust Thalyssra, leader of the Nightfallen. Despite their differences, as well as the Nightborne's efforts to take advantage of them, the groups do ultimately work together and march against the Nightborne together, with Khadgar marveling at how much their teamwork improved.
Command & Conquer: Tiberian Sun: Firestorm GDI and Nod temporarily join forces to defeat CABAL, both sides not too happy about it, and go their separate ways after CABAL is defeated.
Jade, Tear and Anise each suffering this with Luke for a while, when they rejoin him post-Akzeriuth. They're all justifiably angry with him, and clearly don't trust him anymore, and they're mostly working with him for convenience or by coincidence. The only exception is Guy, who went back to Luke voluntarily. And don't worry, they all get better.
This trope also applies to the sequence just before this, in which Asch takes Luke's place to investigate Ortion Cavern with Natalia, Jade and Anise. He's a Jerkass the whole time. And it continues through the rest of the game. He becomes the Sixth Ranger after the Akzeriuth incident, but opts to work by himself because he can't stand his "teammates" (particularly Luke); Natalia is the only exception.
Natalia and Jade have one of the most contentious relationships among the party and seem to view each other with genuine contempt. Unlike other examples in the game, it never seems to get better and the two never have a moment where they show they care about each other.
In Fire Emblem Awakening the player can command certain units to pair up and work as a team such as Chrom and Gangrel, even though in the story those two clearly hate each other.
In Tekken 4 Kazuya and his father Heihachi briefly team up in order to fight a squad of robots. They perform well together as a team and are in perfect synchronization, and only when the battle is about to end with an explosive finale does Kazuya betray his father and leave him to die in a massive explosion. The fact is that Kazuya and Heihachi despise each other to the point that they each tried to kill the other. In the Tekken Tag Team spin offs the player can pair up Jin with Kazuya his father and like in the previous generation Jin wants nothing more than to hurt Kazuya and Kazuya returns that gesture. Their victory poses actually have them staring each other down, while in another Jin attempts to punch Kazuya before he flies away.
The allied races in Guild Wars 2 tend to clash quite often due to their greatly different social, religious, and moral differences. This is especially pronounced between the Charr and humans due to their long history of war with one another. Only renewed aggression from the Elder Dragons convinces them to put aside their differences.
Ratchet and Clank through the latter half of the first game. The two start on friendly enough terms, but after Qwark's betrayal Ratchet becomes excessively bitter and bent on getting revenge or goofing off rather than going after Drek like Clank wants to and blames Clank for falling for Qwark's trap, while Clank becomes irritated at Ratchet's lack of responsibility, leading the two to personally start clashing. The only reason they remain together is they need each other to accomplish their respective tasks, and both make it clear they're not happy it. They're able to get over things by the end of the game and through the rest of the sequels they're back to being friends.
In Captain Morgane and the Golden Turtle, Morgane and her father's first mate, Diego, don't much get along, since he considers her unfit for the responsibility her father has given her. However, they find common ground on the need to get Morgane's father to come to terms with his wife's death. The teamwork gets less forced after they succeed at that.
Persona 3 initially has a fair amount of friction between the second-years and the third-years who are the founding members of SEES (especially Mitsuru, whose family was responsible for the incident that created the Shadows SEES fights), particularly since Yukari accuses the latter group of ordering the others around while keeping secrets from them. In the spinoff Persona Q: Shadow of the Labyrinth, which pairs the casts of Persona 3 and 4, on the Persona 3 route, Yukari notes how much closer the cast of the fourth game is, and gradually gains the resolve to do something about it. In the end, though, the group becomes a cohesive force, and Yukari and Mitsuru eventually become friends.
During The Answer, virtually no one trusts Metis, Aigis' "sister," since Metis starts off attacking them, and they see her as first and foremost concerned about Aigis. On a party-wide scale, the group's teamwork regresses as a result of lowered morale following the protagonist's death, and near the end, they end up fighting each other to resolve their dispute over what to do with the Keys of Time. They come to their senses, though, in time to defeat the final boss and return to their own time.
Granblue Fantasy: The Luminary Knights and Gilbert mutually despise each other with the only thing keeping them from descending into fighting being their loyalty to the True King.
Grand Theft Auto V: The main trio all work together, usually because the FIB are making them, despite Trevor's anger at Michael faking his own death, Michael not wanting anything to do with Trevor and wanting to prevent him learning the truth about North Yankton, with Franklin caught in the middle of their bickering, much to his own annoyance. It's made even worse when Trevor finds out Brad died and was buried in Michael's place.
Shin Megami Tensei IV: Apocalypse has humans, the angels led by Merkabah, and the demons led by Lucifer, all working together in order to defeat the Divine Powers, who have stepped into the picture as the greatest threat to all. The three temporarily-aligned factions make it clear that they still hate one another's guts and are only putting in as much teamwork as they absolutely need to; Lucifer and Merkabah by nature of being opposites to each other and humans against Lucifer and Merkabah due to the sides they represent (Chaos and Law, respectively) always using humans as pawns instead of having humanity's best interests in mind.
In Overwatch, some combinations of Heroes on the same team lead to conversations where it's clear that the involves Heroes are not too thrilled about having to work together:
Widowmaker and Tracer:note Tracer had tried to stop Widowmaker from assassinating a major public figure, without success.
Widowmaker: It looks like we will be working together. Tracer: Don't think I'm happy about that.
Symmetra and Lúcio:note The favela that Lúcio comes from was the target of a major corporation — the one Symmetra works for — that profits from making land redevelopments, destroying neighborhoods and cities if the people of those reject the "improvements".
Symmetra: To think, I would have to work with a street ruffian. Lúcio: I'm not all that excited about this arrangement either.
In Divinity: Original Sin II, you can have Sebille, a woman who was enslaved by the lizardfolk and forced to kill her own kind resulting in a burning hatred of lizards and slavery, in the same party as The Red Prince, an exiled lizard prince (exiled for consorting with demons, if you're curious) who has no problem with the idea of slavery and actually suggests that he should execute Sebille for breaking her bonds in their second meetingnote In the first, he considers taking your main character as his own personal slave, which doesn't exactly help their relationship if your main character is Sebille. Needless to say, they don't get along at all well, though, given enough time, they can become Fire-Forged Friends, with The Red Prince even teaming up with Sebille to kill her former master.
In DOOM (2016), Doomguy and Samuel Hayden both want to defeat the invading demons and save the universe, but that's pretty much the extent of any agreement between them. Hayden wants to use the energy from Hell to provide power for all humanity, while Doomguy knows said energy is more trouble than it's worth and destroys everything relating to the demons. Hayden can only just barely hide his contempt for Doomguy, while the latter doesn't even bother trying and only agrees to work with Hayden at all because he's forced to. Once the demons are beaten and the Hell portal closed, Hayden almost immediately backstabs Doomguy by teleporting him to another realm where he can't get in the way of further research.
The tag-team mechanic of BlazBlue: Cross Tag Battle means it's possible to make two-man teams of characters who absolutely hate each other, most of which involve at least one character from the more volatile BlazBlue and Under Night In-Birth series (the playable Persona and RWBY characters as of the 1.5 update are all True Companions, so they're mostly exempt from this). Some of these characters will have in-battle interactions, or meet in story mode, emphasizing that they're unhappy with their current team up.
On the BlazBlue end, there's no love lost between most characters. Pairing Ragna with Jin, Hakumen, Hazama, Nu, Azrael, Tsubaki, and Platinum means pairing him up with his biggest headaches. Most other characters have personal reasons to hate Hazama, are afraid of Azrael, and can't stand Nu. Jin and Platinum also deserve special mention, as Jin tends to rudely dismiss or threaten most people he's paired with, while Luna's brattiness wins her no favors.
The UNIB characters have less problems teaming up, but most belong to rival factions and thus prefer not to work together any longer than they have to. Linne and Orie are almost seething in their shared intro, hardly anyone trusts Gordeau, Merkava is treated with suspicion and fear, and Carmine hates everybody.
The 2.0 update adds an antagonistic character from each of the four main series, and all of them care little for getting along with anyone. Susanoo makes it clear that his ally is next on his "to kill" list, Adachi revels in pissing off the other three people present in the fight, Hilda is too arrogant and dumb to care about who she's fighting with, and Neo gets a kick from tuning out her partner and letting them flounder.
Valkyria Chronicles 4: Minerva hated protagonist Claude ever since they were at the military academy together: no matter how hard she worked, he was always better. However, she is also a sufficiently responsible officer to accept that he is better than her, and recommends him for promotion over her at a point in the story, and agrees to serve under him in Squad E.
Unless they hit 100 Stress and become Discordant, the Sisters are a case of this located within a single body: the Warrior and the Scholar cordially detest each other, but are willing to work together because if the body dies, so do the both of them.
Any party including the Thrall. The Thrall is such a bullying Jerkass that one of his camping skills consists of the other party members chaining him to a tree because it's easier than dealing with his shit.
Destiny: Cayde-6 and Eris Morn are both Guardians and are both loyal to the Last City. Those are the only things they even remotely agree about. The two virulently hate each other, with Cayde thinking Eris is a potentially-traitorous nutjob who shouldve never gotten her position, while Eris thinks Cayde is an irresponsible moron who has no idea what hes doing. Their only real interactions consist almost entirely of insults, and their grudge gets even worse after Cayde and the Young Wolf steal (and accidentally destroy) Eris ship as part of an Indy Ploy gone wrong. By the time of the second game, Cayde pretty openly admits that he thinks Eris wants him dead and even devotes a section of his will to saying that if Eris is the one who killed him (she isnt), then he is totally unsurprised.
In The Division 2, the Hyenas are a loose coalition of gangs that roam across Washington D.C. to prey upon the weak, and their leaders, the Council, all hate each other, and would gladly stab each other in the back when the opportunity presents itself. The only reason why theyre working together, is so that they wouldnt get overrun by the True Sons, which is made up of JFT forces who went rogue, many of whom are military veterans, the Outcasts, fanatical carriers of the green poison who were wronged by the government, and the Division. Of course, when the Agent assaults their stronghold, they each go after them one by one, and each get picked off one at a time, with the final boss not caring about their deaths.