One idea could be that the animation gains self - awareness and tries to create its own world within the digital realm, away from the animator's control. This would lead to a conflict as the animator wants to bring it back to the original plan.
The obvious main characters would be the animator and the animation itself. The animator could be a young, creative person who is just starting out and is still learning how to control their creations. The animation could be a simple character that was initially designed to be a friendly helper but then turns against the animator.
Perhaps there is a magical rift that causes the two teams' worlds to merge, and they initially misunderstand each other and start fighting. But as they learn more about each other's motives and powers, they team up to face a greater threat that emerged from the rift.
Maybe they are forced to team up against a common enemy, like a powerful new villain in the city who is threatening their usual heist targets. At first, they don't trust each other but gradually learn to work together. For example, Catwoman's knowledge of the Gotham underworld and Blackcat's experience from her own city could combine to defeat the foe.
One idea could be a misunderstanding. Maybe a villain manipulates information to make Batman think Nightwing has turned bad. So, Batman starts to hunt Nightwing, while Nightwing is confused and has to prove his innocence.
One idea could be a world where humans and Pokemon have to compete in a series of challenges to share resources. Another could be a Pokemon rebellion against humans who have been mistreating them.
One idea could be that Mario and his friends are transported to the RWBY world and they have to team up with the RWBY characters to fight a common enemy like a powerful Grimm that has some sort of connection to the Mushroom Kingdom's villains. Maybe Bowser has made a deal with this Grimm to take over both worlds.
Maybe a fanfic where Naruto and Boruto are pitted against each other in a virtual reality battle. It could be part of a training exercise that gets out of control, and they start using their real skills and emotions, leading to a intense and revealing fight.
One idea could be a team - up between Ruby from RWBY and the Red team from Red vs Blue. They could face a common enemy that requires both their unique skills. For example, a new type of Grimm that has advanced technology, and the Reds' combat knowledge combined with Ruby's speed and scythe - wielding abilities would be needed to defeat it.
One idea could be a misunderstanding. Maybe some false information makes Batman think Wonder Woman has been compromised and he has to stop her. Another could be a competition for a powerful, mysterious artifact that they both believe they should safeguard. And a third idea could be a mind - control situation where Wonder Woman is being controlled by an enemy and Batman has to fight her to break the control.
A territorial dispute could be another plot. Black Cat has been operating in a certain part of the city for a while, and Catwoman moves in. They start a battle of wits and skills to see who gets to claim the area as their own hunting ground for valuable items. This could involve a series of rooftop chases and close - quarter combat scenes in the city's seedy alleyways.