A really interesting plot for Vilgax x Ben fanfiction could be that Vilgax discovers a way to clone Ben and tries to create an army of Bens to do his bidding. Ben then has to not only stop Vilgax but also deal with his clones. It could be a story full of action and self - discovery for Ben as he battles his own clones. Another plot could be that a powerful alien entity curses Vilgax and Ben to share a body for a period of time. This forces them to understand each other on a deeper level as they struggle to co - exist and figure out how to break the curse. And, a fanfiction could also be about Vilgax falling in love with a human (maybe someone related to Ben) and how that changes his relationship with Ben, from pure enmity to a more complex emotional state.
Well, a plot could be that Vilgax gets amnesia and Ben has to decide whether to take advantage of this or help him. This could lead to a whole new dynamic between them as Ben tries to figure out what to do. Also, a fanfiction could explore what would happen if Vilgax became a mentor to Ben in a strange, alternate universe. They could train together and Vilgax could pass on some of his knowledge, but also try to manipulate Ben for his own ends. Or, perhaps a story where Vilgax and Ben are both stranded on a strange planet and have to work together to survive, all while dealing with their mutual distrust.
Gwen could be a great addition. She could be the voice of reason when Ben and Vilgax are at odds or she could have her own powers play a role in the story. Grandpa Max is also a good choice. His wisdom and experience could add depth to the fanfiction, especially when dealing with Vilgax. Another character could be Kevin. His ability to absorb energy could create some interesting interactions with Vilgax and also provide a different kind of friendship or rivalry dynamic with Ben.
Perhaps a story where an old enemy of Ben's targets Rook to get to Ben. Ben feels guilty and protective. They go on the run, hiding in different places across the galaxy. Along the way, they meet some interesting characters who help them. In the end, they face the enemy together, with Ben using his Omnitrix and Rook using his upgraded Proto - Tool to defeat the bad guy.
One idea could be that the Nemetrix starts malfunctioning and gives the alien predators it controls some of Ben's Omnitrix powers. This would create a whole new set of challenges for Ben as he has to deal with enemies that are a strange mix of the two technologies.
One idea could be the reader having a unique alien ability that Ben discovers during an adventure. They then team up to fight a new villain that is immune to Ben's usual alien forms.
One idea could be that Mal and Ben face challenges in their relationship due to the unexpected pregnancy. Their kingdoms might have different reactions, with some being supportive and others worried about the future of the united kingdoms. They have to work together to prove that they can handle this new chapter while also dealing with any internal doubts.
Perhaps a fanfic where Ben and Rook accidentally swap abilities. Ben has to deal with Rook's weaponry and combat skills, while Rook tries to control the Omnitrix. It would be full of comical moments as they struggle to adapt, but also a chance for them to learn more about each other's strengths and weaknesses.
One idea could be exploring Alien X's internal conflict between Bellicus and Serena in a new situation. For example, when faced with a moral dilemma on a planet where two species are at war and both have valid reasons for their actions. Another plot could be Alien X having to deal with a powerful new enemy that can somehow disrupt his omnipotent powers. Maybe this enemy has the ability to split Bellicus and Serena's consciousness further, causing chaos within Alien X.
Another interesting plot could be that Myaax comes from a parallel dimension where she has different powers. In the fanfiction, she accidentally crosses over into Ben's dimension. Ben, being the hero he is, tries to help her get back home while also learning about her unique powers and how they could be useful against some of his usual foes. For example, her powers might be related to energy manipulation, which could be used to enhance the Omnitrix's functions.
For 'ben 10 x overs fanfiction', a great concept would be a crossover with the DC Universe. Picture Ben 10 meeting Superman. Ben could be in awe of Superman's powers, and they could team up to stop Lex Luthor who has somehow gotten his hands on some of Ben's Omnitrix technology. Or a crossover with the Justice League where Ben's unique abilities add an interesting dynamic to the team. He could transform into different aliens to complement the skills of each League member.
One idea could be that Ben discovers a new and powerful alien form in the Omnitrix that has abilities he's never seen before. He has to quickly learn to control it to defeat a new and dangerous villain.