Here's a plot idea. A powerful energy source is discovered in Gotham. Batman is studying it when it explodes and sends out a shockwave that alters reality. Suddenly, Gotham is merged with parts of the Avengers' world. Batman and the Avengers have to figure out how to separate the two worlds again while dealing with the chaos that ensues. Another idea is that a mad scientist creates a clone of Batman and sends it to the Avengers' world to cause trouble. The real Batman has to convince the Avengers that he is the real one and then work together to stop the clone. And finally, a plot where a dark magic user is draining the life force from both Gotham and the Avengers' world. Batman and the Avengers must find the source of this magic and put an end to it.
A great plot could involve a time - travel aspect. Batman discovers a device in the Batcave that sends him back in time to the early days of the Avengers. He has to work with a young and inexperienced Avengers team to stop a threat that, if not stopped, will change the future in a bad way. Maybe this threat is an ancient evil that was sealed away but is now being awakened. Or, there could be a plot where Batman's rogues gallery teams up with some of the Avengers' villains. The combined forces of villains create a huge problem, and Batman and the Avengers have to put aside their differences and strategies to take them down. Also, a plot where an alien race is interested in Batman's technology and kidnaps him. The Avengers rescue him, and in return, Batman helps them upgrade their own tech to fight off the alien race's invasion.
One idea could be Batman using his detective skills to uncover a hidden threat that the Avengers initially overlook. For example, he might notice some small, seemingly insignificant details during a battle scene that lead him to a much larger conspiracy.
Maybe in the fanfic, Batman's rogues gallery somehow teams up with some of the Avengers' villains. This forces Batman and the Avengers to work together. Batman could introduce his unique gadgets and combat style to the Avengers, while they could show him their superpowers up close. For example, Iron Man could be intrigued by Batman's utility belt and try to create his own version of some of the gadgets.
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 exploring what if Loki had an unexpected ally within the Avengers. Maybe a character who was initially on the heroes' side but got swayed by Loki's charm or promises.
In this fanfic, there could be a scenario where Batman is exposed to Kryptonian technology that gives him some Kryptonian - like abilities temporarily. A Kryptonian comes to Earth to study this anomaly. They start off as adversaries but as they learn more about each other, they find that they can work together to protect Earth from a greater threat that only their combined skills can defeat.
One plot idea could be that the Inhumans' city of Attilan is in danger and the Avengers are called in to help. The Inhumans are initially hesitant to accept their aid due to their differences, but they soon realize they need to work together. Another idea is a young Inhuman with a powerful but uncontrollable ability is found by the Avengers. They try to help the Inhuman learn to control it while also protecting them from those who would use their power for evil.
One possible plot could be that Batman's Gotham is threatened by a powerful villain who has some connection to the Avengers' universe. Maybe Loki decides to cause chaos in Gotham as part of a larger plan against Earth. Batman, being the detective he is, starts to investigate and soon realizes that this is no ordinary criminal. He then somehow gets in touch with the Avengers, perhaps through SHIELD's intelligence network. Together, they combine their skills and resources to take on Loki and his minions. Batman's stealth and strategic mind would complement the Avengers' superpowers.
A plot idea could be that Poison Ivy creates a new type of plant - based virus in Arkham that only affects humans who are harming the environment. Batman has to find a way to stop the virus from spreading while also dealing with Ivy's strong beliefs. Another idea is that Ivy discovers a rare plant in Arkham that she believes can save the planet, but it's in a highly guarded and dangerous area. Batman and Ivy might have to work together to retrieve it.
One idea could be an imagine where a new superhero joins the Avengers. They have a unique power that the team initially struggles to understand but eventually learns to utilize effectively. For example, a hero with the power to manipulate time on a small scale, like being able to slow down time for a few seconds during a battle.
A more complex plot could involve the Flash's speed force interacting with the Infinity Stones. The Avengers might be trying to figure out how to use or contain the power of the speed force in relation to the Stones. This could lead to all kinds of conflicts and alliances within the story, as different characters have different ideas about how to handle such a powerful and unknown combination of forces.