Another plot could be that the Dark Elf steals one of Ben's Omnitrixes (if there are multiple in the story). Ben then has to track down the Dark Elf without the use of his usual alien forms. He has to rely on his wits and the help of his friends like Gwen and Grandpa Max to get it back.
Maybe the Dark Elf is actually a misunderstood being. In the fanfic, Ben could discover that the Dark Elf was forced into doing bad things because of some other powerful and evil force. So, Ben tries to help the Dark Elf break free from this control and they end up becoming allies.
A really interesting plot could involve a time - traveling aspect. Ben and Julie accidentally travel back in time to when Ben first got the Omnitrix. They have to be careful not to disrupt the timeline while also trying to find a way back to their own time. Along the way, they could meet younger versions of characters they know and have some really fun and emotional interactions. This could also lead to Ben learning some important lessons about his powers from his past self.
A plot could involve a dark elf noble trying to gain more power within the dark elf society through political intrigue and backstabbing. Or it could be about a dark elf warrior who has a change of heart and tries to break away from the cruel ways of his people. There could also be a fanfiction where dark elves team up with other races, like the skaven, for a common goal, but with their own hidden motives.
Another plot could be that a new villain emerges who has the power to control both human and Myaxx technology. Ben and Myaxx must figure out a way to break this control and stop the villain from taking over the galaxy. They start by gathering intelligence on the villain's lair and formulating a plan that utilizes Ben's shape - shifting abilities and Myaxx's knowledge of her own technology.
One idea could be that as a girl, Ben has to face different social challenges while still using the Omnitrix to save the day. For example, some might underestimate her because of her gender, but she proves them wrong with her heroic deeds.
One idea could be that Ben, using his alien forms, has to battle Dracula's minions in a spooky castle. Maybe he teams up with some local vampires who oppose Dracula's tyrannical rule. Another could be that Dracula tries to turn Ben into a vampire to use his alien powers for his own evil deeds.
A plot could involve a group of young Highbreed who are curious about Earth and its cultures, and they secretly befriend Ben. This would lead to a series of adventures where they have to hide their friendship from the more traditional and hostile Highbreed. They could learn a lot from each other, and Ben could teach them about the value of diversity and cooperation.
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.
Maybe a story where Ben teams up with some of his alien enemies against a greater threat in space. They could be in a situation where they have to fight a powerful cosmic entity that wants to destroy all known planets. Ben would have to convince his former foes that they need to work together by showing them the magnitude of the danger.
One idea could be exploring an alternate universe where Ben gets the Omnitrix at a much younger age and has to learn to control it while dealing with school bullies who are after his power. Another could be a story where the Omnitrix malfunctions and starts giving Ben alien forms that are hybrids of different aliens he already has access to.
One idea could be Ben using his alien forms in a virtual reality gaming world. He could face off against digital versions of his enemies and have to use his unique alien abilities to progress through levels.