Maybe the reader is from a different dimension where the Omnitrix functions differently. Ben has to figure out how to work with the reader to get back to his own dimension while facing threats in the reader's world. For example, there could be new types of aliens there that are both allies and enemies.
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.
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.
Well, you could write a 'ben 10 omniverse fanfiction' where Ben loses his Omnitrix and has to rely on his wits and the help of his friends to still fight the bad guys. Or perhaps a story where the Omnitrix starts evolving on its own and gives Ben new and unexpected powers. Also, a plot where an old enemy from the past returns with a new and more dangerous plan.
A more character - driven plot could be about Ben trying to help an alien species that is being persecuted in the Omniverse. He uses his different alien forms to understand their culture and problems better. Along the way, he discovers that there are some dark secrets in the Omniverse's politics that are related to this species' situation. This would allow for a deeper exploration of the Omniverse's world - building and Ben's character growth.
Another plot might involve Ben and Kai getting accidentally transported to a parallel dimension where things are very different. They have to find a way back home while also dealing with the strange new versions of their friends and foes. Along the way, they discover new things about each other and their feelings start to change in this unfamiliar setting.
Maybe in the fanfiction, Esther gets into trouble while exploring a dangerous part of the Omniverse. Ben discovers her plight and decides to rescue her. As he does, they find themselves in a situation where they are trapped and have to rely on each other to escape. During this time, they share their hopes, dreams, and fears. Ben realizes that Esther is more than just a friend, and Esther sees Ben in a new light. Their relationship blossoms from there, with them having adventures together and supporting each other in the Omniverse.
Some good ones include 'Rook's Protective Side'. In this fanfiction, the reader is in danger and Rook shows his very protective side towards the reader. It's a great read if you like to see the relationship develop from a more protective angle. Additionally, 'A Day with Rook' is a lighter fanfiction that just shows a normal day in the life of Rook and the reader, with some cute interactions and dialogues.
One possible plot could be that Esther gets caught up in an alien conspiracy in the Omniverse. Ben, being the hero, steps in to save her. As they work together to uncover the truth behind the conspiracy, they start to fall for each other.
Well, in a 'Ben 10 Omniverse Ben x Kai' fanfic, perhaps it could start with Kai joining Ben on one of his inter - dimensional adventures. Along the way, they encounter various challenges that test their relationship. Ben might use his Omnitrix in creative ways to protect Kai, and in the process, they realize their mutual attraction. For example, when they are trapped in a strange alien world, Ben has to transform into different aliens to find a way out while also keeping Kai safe from the local dangers.
One great Ben x Kevin fanfiction could be about their adventures in a parallel dimension. In this story, they might face new aliens and challenges that test their friendship even more. Maybe they find a powerful alien artifact that only works when they combine their unique abilities, leading to a deeper understanding of each other.
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.