In Hogyoku Ex Machina, Yoruichi is surprised when she finds out that the Vizards fought alongside Soul Society against Aizen in the original timeline, since they have no reason to like them. Ishida suggests it was because of this trope.
Under the Bridge: Widget has taken several attempts at killing Gadget. Now Chip calls her on her submarine Albacore on the radio, alerting her that Gadget is out to attack and sink Albacore with a self-made, air-dropped torpedo. But the call comes in time: A young squirrel from Widget's crew named Andy injured an ankle on an unprotected chain, and now Widget needs Gadget and her aircraft to take him to a hospital. Meanwhile, when Widget comforts Andy, this also helps trigger her Heel-Face Turn.
In Carpetbaggers, when the newly-crowned Pevensies need backup to fight a horde of the Witch’s creatures, they recruit the rebels who were holed up in the castle bullying and blackmailing local Narnians.
In Aeon Natum Engel, during the Herald fight, the Migou recall some of their forces so that the NEG Military, with the newly freed-up forces, can assist in defeating the Herald. Humanity doesn't return the favor.
This happens in the Naruto/Justice League crossover Connecting The Dots when Naruto and Sasuke team up against a REALLY big threat.
Burning Black: Anti-Cosmo, and by proxy every anti-fairy he commands, allies with Team Turner against Remy and the Pixies in Act 3. He even outlaws the use of bad luck on Timothy directly; indirect bad luck is still fair game. The relationship is creeping into Friendly Enemy territory, which makes Cosmo and Wanda very nervous as Timmy's exposure to anti-fairies affects his personality and allows him to use black magic while giving him immunity to anti-magic waves.
A Shadow Of The Titans: Jinx briefly teams up with the Titans after Mumbo captures both Jade and Starfire and forces them to be his "assistants". Jinx describes it as "sharing a mutual problem", and as soon as Mumbo is defeated she grabs Jade and runs off.
The possible Bad Future glimpsed in the "Destiny" interlude has another apparent example: whatever "Omega" is, it's so bad that the Demon Sorcerers and the Eight Immortals team up with each other and Good!Jade to stop Evil!Jade from releasing it.
Jade and Raven teaming up against the Master of Games.
In Never Had A Friend Like Me, the Pixies and the Anti-Fairies have mutually exclusive goals for the world. They have, however, teamed up together temporarily in order to remove an obstacle to both their plans: Timmy Turner.
Later, they join Norm, Timmy, and his fairies in trapping Bob in another dimension.
A Brief History of Equestria: When Wind Whistler led a coup against Commander Sullamander, she recruited help from Star-Swirl the Bearded and the few unicorns loyal to him. True, Star-Swirl was open-minded and friendly with the other tribes, but that's still members of one nation asking help from members of a rival nation to overthrow their leader.
Played straight when the Changeling Princess Pupa allies with Applejack's group to stop (her sister) Chrysalis' invasion of Gildesdale, with the promise that afterwards she'll also ally her people with the ponies against Cetus.
At the climax of Rolling in Beaches, Spike convinces the hippocampi and Scaly Back River Clan dragons to put aside their differences in order to stop all the dragons and Mane Six turned into monsters by the Rainbow of Darkness.
Clover's story in the 7 Dreams/Nightmares collection reveals that eons ago, a group of Eldritch Abominations escaped the loss of their own reality by entering the POV multiverse with the intention of absorbing all beings into their Hive Mind in order to torment them for all eternity. This offended bothFauna Luster and Entropy — the former because She's a strong believer in free will, and the latter because it would potentially prevent the end of all things She embodies and desires — leading to Them, Their Mates, and Their respective children working together to defeat these things and seal them beyond the Gates of Tartarus. It's noted in-universe that this is the only time the two of Them have ever agreed on anything.
During the Wedding Arc, while they're unaware of it, the heroes' efforts are being aided from the sidelines by Discord and Nightmare Diamond, who are aware that if Chrysalis succeeds in her plans, she'll be powerful enough to be a threat even to them.
During the Finale Arc, when Discord and his allies begin their endgame plan, it's so horrifying that a group of alternate dimension Nightmares show up to help stop them.
Kyuubi: "Because I hate. There are many things I hate. The Sage of the Six Paths. Madara Uchiha. Hashirama Senju. Mito Uzumaki. Minato Namikaze. The toads. Kushina Uzumaki. But more than anything else, I hate the Shinigami. He stole over two thirds of my power, and claimed the Namikize's soul in return, a violation of his own laws and rights. The Shiki Fuin, the contract with the Shinigami, works on a simple basis. A soul for a soul. He did not take my soul, merely my power. When I was sealed, he had nothing to do with it. By the ancient laws, he should have let the Namikaze go, or at least send him to the Pure World, and return my power to me. But he didn't, breaking ancient law. ... You see, he has stolen from me, so I will ensure that he suffers for it! You Naruto, are the key of my vengeance. Through you I will make him suffer. All I ask is that you call back many, many souls, I don't even care for what, and in return, I will give you what all other jinchuuriki can only dream of, my full support."
Villain example: Although Brox and Co. and the Raleka in With Strings Attached aren't exactly mortal enemies, they dislike each other considerably. Brox and Co. are contemptuous of Ketafans in general, and the Raleka hate that the skahs want to use the sacred Vasyn for stupid purposes. However, they work together against the four because the Raleka cannot do certain things without Brox's help. We find out later that Brox and Co. were planning to betray the Raleka, but Paul and George inadvertently screwed this up for them.
One issue of Ultimate Spider-Woman: Change With the Light has petty criminal Blizzard teaming up with Spider-Woman to help her protect the innocent people in danger during an invasion of New York City by an army of Brainwashed and Crazy super villains. Taking inspiration from the Darkwing Duck episode where DW teamed up with Megavolt (see below), Blizzard points out that if New York is destroyed, there'll be nothing left for him to rob.
Peace Forged in Fire: Praetor Velal of the Romulan Star Empire becomes disgusted at the underhanded attempts of the Tal'Shiar to disrupt the peace talks between the Empire and the Romulan Republic, and joins with his opposite numbers to take them down. During the talks they also prepare command protocols for joint military operations against enemies like the Undine and Borg.
Reality Is Fluid: Eleya is able to convince an Undine commander that the Federation et al. were not responsible for the attacks on Undine spawning pools and hatchlings that sparked the current war, and that faction begins targeting the Undine that have been infiltrating the Alpha and Beta Quadrant powers and agrees to join the fight against the Iconians when the time comes.
In the fic Safe and Sound, Kirk and Khan pull one of these, similar to the one they pulled in the second film, in order to save the kidnapped Nyota Uhura, Joanna McCoy and Lucille Harewood. This time, Khan doesn't betray him.
In A Far Green Country, Durus and Surad were enemies of Elden and Nellas, but these four quickly become allies when they are chasing a common enemy.
In the Transformers fanfic A Child Shall Lead Them, the Dinobots end up teaming up with Galvatron and Cyclonus to escape the Quintessons. Galvatron ends this alliance fairly quickly when he literally stabs Pterodactus Prime (aka Swoop) in the back.
In CenotaphPurity and Skitter team up to fight the ABB. On one hand a flying Blaster, ex-Nazi single mother. On the other, a ruthlessly intelligent, highly resourcefull teenage highschool student and newly-minted orphan with dreams of being a hero. Together, they fight crime!