A crossover with Teen Titans would also be cool. Rex could interact with the Titans in their tower. His combat skills and nanite powers would add a new dynamic to the team. Maybe he could help them fight against a powerful villain like Trigon by using his nanite - based creations to hold off Trigon's minions while the Titans use their powers to directly combat him.
One idea could be a crossover with Ben 10. Rex's nanites and Ben's Omnitrix could lead to some interesting power clashes and team - ups. They could face a common enemy that requires both their unique abilities to defeat. For example, an alien - nanite hybrid villain.
In a fanfiction crossover, they could end up in each other's universes by accident. Ben finds himself in a world full of EVOs and has to rely on Rex to get back home. Meanwhile, Rex is intrigued by the Omnitrix and tries to figure out how it works. They face many challenges together, like dealing with Rex's old enemies who see Ben as a new target.
Another story could be set in a post - apocalyptic world where vampires have emerged as a result of some mutagenic event related to the nanites. Rex, being the only one with the ability to control his nanites, has to find a way to coexist with the vampires. He could encounter a vampire who was once a scientist and together they try to reverse the vampiric transformation in some people.
One idea could be a crossover where Generator Rex's nanites interact with the X - Men's mutant powers in unexpected ways. Maybe the nanites start to adapt and mimic some of the mutant abilities, causing chaos and confusion among both groups.
One idea could be that Naruto and Rex meet in a dimension where their worlds collide. Naruto's chakra powers and Rex's nanite abilities could create some really interesting battle scenes as they team up against a common enemy, like an evil organization that wants to control both their worlds.
Another plot could be that an interdimensional rift opens up, and it's causing chaos in both Ben's and Rex's worlds. They discover that the source of the rift is related to the technology of both the Omnitrix and the Nanites. Together, they journey through the rift to find the cause and close it. Along the way, they meet alternate versions of themselves and their friends, which adds an interesting twist to the story.
One idea could be that Ben and Rex have to team up to stop a new villain who has the ability to disrupt both Omnitrix - based powers and Rex's nanites. They start off not trusting each other but as they face challenges, they learn to work together.
One possible fanfiction could be about Rex's adventures in a new, uncharted area where he discovers a strange new type of E.V.O. He has to use his powers in creative ways to deal with it and learn more about this new threat or ally.
Definitely include Six. He's Rex's mentor and his combat skills and knowledge would be valuable in any crossover. If it's a crossover with a superhero team, he could offer strategic advice.
A fanfic could focus on Noah's perspective of being Rex's friend. Maybe Noah starts to feel a bit overshadowed by Rex's powers and has to deal with his own insecurities while still supporting Rex in their adventures. For example, during a mission where Rex is getting all the glory, Noah could be the one who actually figures out the key to defeating the EVO, but no one notices at first.
Fanfiction about Rex and Six could also involve a mission where they are sent undercover. They have to pretend to be ordinary people in a community that is on the verge of being overrun by E.V.O.s. They need to figure out how to stop the E.V.O.s without blowing their cover, and in the process, they learn more about each other's personalities outside of the battlefield.