A great plot could be Wolverine being forced to team up with the Avengers to stop a powerful mutant - hating villain. Wolverine's healing factor and combat skills would be a huge asset, but his distrust of non - mutants could create internal conflict within the team. Maybe Wolverine has a past encounter with the villain that the Avengers don't know about, and this knowledge could be crucial to their victory.
How about a plot where Wolverine is accidentally sent to an alternate universe where the Avengers are very different? He has to find a way to get back home while also dealing with this new - fangled Avengers team. The Avengers, in turn, are intrigued by this strange, feral man with claws. They try to understand his powers and motives, and together they face a threat that spans across multiple universes.
A cool plot could be that Wolverine's past comes back to haunt him during an Avengers mission. His time in Weapon X could be related to the new threat the Avengers are facing. So, the Avengers have to help him deal with his demons while also fighting the enemy. Or perhaps Wolverine discovers a connection between a mutant he knew and an Avenger, which leads to a mystery they have to solve together.
One idea could be a Wolverine and Batman crossover. Wolverine could find himself in Gotham City and team up with Batman to take on a common enemy like Ra's al Ghul who is interested in Wolverine's healing factor. They would have to combine their skills, with Wolverine's brute strength and healing and Batman's detective skills and gadgets.
One idea could be Wolverine getting transported to the DC universe and teaming up with Batman. They could combine their detective skills to solve a mystery that involves both mutants and metahumans. For example, a new villain is creating chaos in Gotham by using some sort of technology that affects Wolverine's healing factor in strange ways.
One idea could be a crossover with the Doctor Who universe. The Avengers could team up with the Doctor to fight a common enemy that threatens both their universes. Maybe Thanos somehow gets access to Time Lord technology and the combined forces have to figure out how to stop him from using it to rewrite all of reality.
One idea could be a crossover with the Harry Potter universe. The Avengers could visit Hogwarts and interact with the wizards. Maybe Iron Man tries to understand and even improve their magic technology. Another could be a crossover with the Star Wars galaxy. The Avengers team up with the Jedi to fight against a common threat like Thanos and the Sith Lords combined.
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 the Avengers are facing a supernatural threat that they can't understand. So they seek the help of the Winchesters from Supernatural. The Winchesters introduce them to the world of the supernatural, like demons and ghosts. And together they combine their skills, the Avengers' superpowers and the Winchesters' hunting knowledge to defeat the threat.
One idea could be that Daredevil's enhanced senses are needed to track a villain who has a cloaking device that the Avengers' technology can't detect. Another could be Daredevil getting caught in the middle of an Avengers - villain battle in Hell's Kitchen and having to team up with them to protect his neighborhood. Or perhaps Daredevil's legal knowledge helps the Avengers deal with the political fallout of one of their big battles.
One idea could be that Elsa's powers are mistaken for some sort of new super - weapon by the villains in the Avengers universe. So, the Avengers have to figure out if she's a threat or an ally. Another could be that the Avengers get trapped in Arendelle during a mission and have to work with the Frozen characters to get back home. Maybe Thor could teach Kristoff some combat skills while Elsa helps Iron Man with his suit's temperature control system.
Well, a cool plot could involve Spider - Man's identity being revealed to the public and the Avengers having to protect him from various villains who see this as an opportunity to take him out. Or perhaps a situation where an old enemy of the Avengers teams up with one of Spider - Man's foes, forcing the two groups to work together more closely than ever. Spider - Man could also introduce some new tech or fighting styles to the Avengers during their joint adventures.