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.
At first, they could be rivals. Ben might think Rex's nanites are too unpredictable, and Rex could see Ben as a bit of a show - off with his Omnitrix. But as they face common enemies, they start to respect each other. For example, when they're both captured by a powerful villain, they see how the other fights and starts to understand their strengths.
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.
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.
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.
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.
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.
It could be Ben when he transforms into Alien X. Alien X has near - omnipotent powers. He can manipulate reality on a cosmic scale. In a crossover, he could potentially use those powers to control the Nanites or even restructure Rex's powers in some way. However, he's also very difficult to control, so it's a double - edged sword.
I think an evil scientist who has found a way to combine the power of the Omnitrix and the nanites in a wrong way could be really interesting. He could be creating hybrid monsters that are very difficult for Ben and Rex to defeat. He would be constantly one step ahead because he understands both technologies so well.
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.
In a post - apocalyptic world, Generator Rex was on a mission. Rex was also exploring the same area. They both heard rumors of the Black Knight. When they finally met the Black Knight, he was not what they expected. The Black Knight had a code of honor. Rex was intrigued and Generator Rex was curious about his technology. They started to exchange knowledge. The Black Knight taught them some ancient combat techniques and in return, Generator Rex shared his knowledge of advanced machinery. Rex learned a lot from both of them and they became friends, vowing to protect the world together.