A plot could be that Joker gets his hands on a powerful and mischievous Pokemon like Ditto. He uses Ditto to create chaos by transforming into various threats. Batman has to team up with a young Pokemon trainer to stop the Joker. The trainer could introduce Batman to different Pokemon strategies along the way.
One idea could be that the Flash has to help Batman track down a super - villain who has the ability to manipulate time. Since the Flash is a speedster, he can move through time - altered situations more easily. Another plot could involve Batman creating a new gadget to counter a meta - human threat, and the Flash accidentally gets caught in its test run, causing some wacky time - space anomalies that they have to work together to fix.
Here's an idea. There could be a powerful magical artifact that surfaces in both cities. It has the power to change reality. Superman, being a man of science, is initially skeptical about its power. Batman, on the other hand, has seen enough strange things in Gotham to know it's dangerous. They have to overcome their differences in beliefs as they race against time to stop different factions in both cities who want to use the artifact for their own gain. Along the way, they also learn more about each other's worlds and form a stronger bond.
One idea could be that Batman and Arrow team up to take on a common enemy like Ra's al Ghul. Since both of them have had run - ins with him in their respective storylines, it would be cool to see them combine their skills and resources to fight against him. Another plot could involve a mystery that spans both Gotham and Star City. Maybe there's a new criminal organization that's using technology from both cities to carry out their evil plans, and Batman and Arrow have to figure out how to stop them while also dealing with the differences in their methods of crime - fighting.
A great plot could involve the two heroes swapping cities for a while. Arrow tries to deal with Gotham's crime underworld while Batman goes to Starling City to investigate a series of strange disappearances that might be linked to a powerful criminal organization there. This would lead to both heroes having to adapt to different environments and crime - fighting styles.
A cool plot might be that a new meta - human emerges who has the power to steal the abilities of other heroes. This meta - human targets the Flash first, leaving him powerless. Batman then has to take the Flash under his wing and train him in more traditional combat skills while they figure out a way to get the Flash's powers back. Along the way, they discover that the mastermind behind this meta - human is an old enemy of Batman who wants to use the Flash's powers to carry out a grand scheme in Gotham.
A great plot could be that Batman, being the master detective, discovers a plot by some unknown force that is targeting both Gotham and the Avengers' main cities. He contacts the Avengers for help. They initially have some trust issues as Batman is a loner and the Avengers are used to working as a team. But as they start to understand each other's methods, they combine forces. For example, Batman's stealth and strategic skills combined with Captain America's leadership and combat skills could make for some really cool fight scenes against the common enemy.
One idea could be that Batman visits Smallville to investigate some strange technology that has been showing up in Gotham and has ties to LuthorCorp. He teams up with Clark Kent, who is still in his early days of understanding his powers. They could have a cool dynamic where Batman is initially suspicious of Clark but then realizes he's a powerful ally.
One plot idea could be that Bella Swan, from Twilight, gets lost in Gotham City. Batman discovers her and at first suspects she's part of some new vampire plot in his city. But as he gets to know her, he realizes she's just a lost girl with her own set of supernatural problems. Another idea is that the Cullens move to Gotham for some reason. Edward and Batman cross paths and Edward's mind - reading ability both intrigues and annoys Batman. They could end up working together to stop a new breed of super - vampires that are terrorizing the city.
Maybe Sonic discovers a chaos emerald has the power to transform Pokemon into super - powered versions, similar to Mega Evolutions. He has to work with Pokemon trainers to make sure this power doesn't fall into the wrong hands. The chaos emeralds' energy could also attract Legendary Pokemon, leading to some epic battles and adventures.
One idea could be that a pokemon ranger is transported to a different pokemon world where the rules are all mixed up. For example, they might find that water - type pokemon can fly. Another could be a crossover where the pokemon ranger teams up with a famous pokemon trainer from the main series to stop an evil organization that's using a new type of technology to control pokemon. And a third idea is a world where pokemon rangers have to compete in pokemon battles like trainers do, which would be a huge change in their normal duties.