A more emotional plot could involve Breach getting injured and Rex having to take care of her. During this time, they have deep conversations about their fears and hopes. Breach might open up about her loneliness as an outcast, and Rex could share his own insecurities about his role as a hero. This could lead to a stronger bond between them.
Another plot could be a time - travel scenario. Maybe Breach accidentally opens a portal that sends them both back in time to a crucial moment in Rex's past. They have to navigate this new time period without changing too much of the future while also dealing with their own relationship dynamics, which are complicated by the knowledge they have from the future.
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.
Maybe a fanfic where Rex discovers a hidden talent of Breach that no one else knew about. For example, Breach is an amazing artist but has been hiding it. Rex encourages Breach to show it to the world, and through this process, their relationship blossoms. It could also involve some challenges from the other members who don't believe in Breach's new - found confidence.
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.
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.
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.
A possible plot could be that the Black Knight is wrongly accused of a crime. Rex and Generator Rex are initially tasked with capturing him. But as they get to know him during the chase, they realize he is innocent. So, they join forces to find the real culprit who is actually a powerful and corrupt figure trying to frame the Black Knight to gain more power in the post - apocalyptic world.
Rex's powers could be used in a unique way if he has to combine his different nanite - based abilities in a new and unexpected manner. For instance, instead of just using his Smackhands to fight, he could use them to create a shield for Breach when she's in danger. This would show his adaptability and his growing concern for her safety.
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.