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In The Gamers Alliance, Kagetsu I begins working with the Grand Alliance against Arawn Losstarot when the Alliance saves Kagetsu's wife Marya from Arawn's stronghold. Likewise a group of clerics of MardŁk and Samachi work with the Alliance against the Northern Horde during the battle of Vanna despite their animosity which stems all the way from the Great War.
In Survival of the Fittest, Shameeca Mitchell and Heath Trennoby enlist the aid of Anti-Villain Bobby Jacks in order to mount a rescue from all around asshole Lenny Priestly. Admittedly Shameeca hadn't met Bobby before this point, but she was well aware that he was a killer.
In Chapter One of Off The Page And Into Life, Gail and Terrence have hated one another since childhood, in no small part thanks to their mutual interest in Henry. However, when MadameBlue begins spreading lies about them, they agree to work together to get rid of her. Gail even lampshades it, remarking that they're Not So Different, and probably would've taken over the world by now if they didn't hate each other so much.
STO Forum: Versus thread (rp) somewhat encourages this. On the one hand, the encounters are somewhat easier with two or more players working together since they can cover for each other, but on the other hand only two characters can get off the planet in the end. Examples so far:
Eleya and Kang join up early on in a swamp after she gets stuck in the mud and he rescues her. Averted in that the two of them actually seem to like each other.
Played straight with the other two. Torpal initially tries to kill 007. 007 shoots him nonfatally in both legs and gives him the option to join up or face a Coup de Gr‚ce. Torpal grudgingly agrees. Breaks down almost immediately when they run into Jem'Hadar and try to use the other as bait. 007 comes out on top and Torpal dies.