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.
Maybe there's a strange energy source that is causing the Omnitrix to malfunction and Rex's nanites to go haywire. They must travel across different dimensions, which are both familiar to their respective shows, to find a way to stop it. Along the way, they meet some of their old foes who are also affected and have to decide whether to help them or not. This would lead to a lot of character development for both Ben and Rex as they deal with moral dilemmas.
A great plot could be that an alien race is interested in Rex's nanite technology and Ben's Omnitrix. They capture both of them and try to extract the powers. Ben and Rex have to use their wits and what little power they can access in the captivity to escape and then turn the tables on the aliens. This would involve some cool fight scenes and also some tense moments of them trying to figure out how to work together in a completely foreign environment.
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.
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.
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 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.
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 idea could be that Rex discovers a hidden power within Fairy Tail that was long forgotten. This power could be related to an ancient magic that only he can unlock due to his unique connection with the guild.
One idea could be that Rex and Breach are forced to team up against a new, powerful EVO that threatens their mutual interests. Along the way, they start to understand each other's pasts and develop a grudging respect. For example, Rex could learn about Breach's difficult upbringing in the Nanite Collective and start to see her in a new light.
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.
A plot idea could be that a powerful organization is stealing both biotech from Generator Rex's world and quirks from My Hero Academia's world. Rex and the heroes have to team up to stop them. Another idea is that Rex accidentally gets transported to the My Hero Academia universe and has to figure out how to get back while also dealing with the chaos of a world full of quirks.
One plot idea could be that Rex's nanites start to interact strangely with the eezo in the Mass Effect universe. This causes unforeseen effects like creating new forms of biotics or causing glitches in mass relays. Another idea is that Rex is mistaken for a new species and is studied by Cerberus, who want to use his nanites for their own evil purposes. He has to escape and team up with Shepard to take down Cerberus once and for all.