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.
To develop their relationship, they could start by sharing their backstories. Ben could tell Rex about how he got the Omnitrix, and Rex could share his experiences as an EVO. This would create a bond between them. Also, they could have some light - hearted moments, like competing in a friendly race or a strength test. Through these interactions, they would grow closer.
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.
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.
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.
There could be a plotline where an ancient artifact is discovered that has the potential to either destroy or save both the world of Ben 10 and Generator Rex. Ben and Rex are drawn to it for different reasons. Ben thinks it could be a powerful weapon against his enemies, while Rex believes it could help him understand more about the origin of nanites. However, they soon find out that there are many forces trying to get their hands on this artifact too. They must protect it from falling into the wrong hands and also decide what to do with it in the end. This would involve a lot of action, adventure, and moral dilemmas for both characters.
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.
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 interesting crossover could be their powers combining in a unique way. For example, Ben could use one of his alien forms' abilities in tandem with Rex's nanites. Maybe Heatblast's heat powers could supercharge Rex's nanite - based weapons. Another aspect could be their personalities clashing and then learning from each other. Ben, being more of a carefree hero at times, could teach Rex to loosen up a bit, while Rex's more serious and scientific approach could help Ben be more strategic in his battles.