One idea could be a story where the Omnitrix is fused with a Pokeball, allowing the protagonist to transform into a Pokemon and use its powers while also being able to capture other Pokemon in a unique way. Another could be a cross - over where characters from Ben 10 (where the Omnitrix is from) end up in the Pokemon world and have to use the Omnitrix to survive and understand the new environment. A third idea is a story where a Pokemon trainer discovers an ancient Omnitrix - like device that gives them the ability to transform into rare and powerful Pokemon forms that no one has ever seen before.
A great idea for a Pokemon Omnitrix fanfiction could be a story set in a future where the Omnitrix technology has been integrated into Pokemon battles in a big way. Trainers now have to not only strategize about which Pokemon to use but also which form to transform into using the Omnitrix. There could be a tournament where the best trainers compete, and they all have their own unique Omnitrix - Pokemon combinations. It could also explore the ethical implications of using such a device in Pokemon battles, like whether it gives an unfair advantage or if it's a natural evolution of the battling system.
You could also write a fanfiction where an OC is accidentally bonded with the Omnitrix in a way that it can't be removed. The OC then has to learn to live with it and use its powers for good, but they face challenges as they are not Ben. They might have to deal with people who are suspicious of them having the Omnitrix and also face enemies who are specifically after the device because of its new and unexpected host.
One idea could be that the Omnitrix malfunctions and gives Ben new, unexpected alien forms with powers he has to quickly learn to control. For example, an alien that can manipulate time in small bursts, which would create really cool scenarios where he has to fix things that went wrong in the past few seconds. Another idea is that a new villain is specifically targeting the Omnitrix and Ben has to protect it while also trying to figure out the villain's motives. Maybe this villain has a device that can nullify the Omnitrix's powers temporarily.
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.
One idea could be exploring a new alien form that wasn't in the original series. Maybe an alien with the power to control time in a unique way. Another idea is to have Ben go on a mission in a completely different galaxy, facing new challenges and enemies.
A possible plot is that the self - inserted character has to deal with the Omnitrix malfunctioning. This could lead to unexpected and sometimes comical transformations. They might transform into a really weak alien in the middle of a battle or into an alien that is completely inappropriate for the situation, like a tiny alien when they need to be strong. As they try to fix the Omnitrix, they learn more about its inner workings.
One idea could be that a character from Fairy Tail finds the Omnitrix and has to learn how to use it without getting overwhelmed by its powers. Maybe they initially use it for simple tasks like getting out of tight spots during a guild mission, but as they get more proficient, they start using it in more complex battles against powerful foes.
One idea could be that the male OC with the Omnitrix accidentally gets transported to an alternate dimension where the Omnitrix functions differently. He has to figure out how to adapt and use it to get back home. Another plot could involve the OC using the Omnitrix to stop an alien invasion that is targeting his hometown specifically. Maybe the aliens are after the Omnitrix's power source.
In some Omnitrix fanfiction, there are crossovers with other universes. For instance, a story where the Omnitrix wielder ends up in the Star Wars universe. They have to use their alien forms to survive in this new and very different environment, facing off against Sith Lords and using their powers in creative ways to interact with the Force.
What if the Omnitrix was actually a gift from a legendary Pokemon? In this fanfiction, Ash is chosen to receive it because of his pure heart and strong will. However, using it comes with a price. Every time he transforms, it drains his energy, and he has to find a way to replenish it. This could involve seeking out special items or places in the Pokemon world. His friends would have to help him manage this new challenge.
One interesting storyline could be about Ben exploring new alien forms that were previously unknown in the official series. Maybe he discovers a form that has unique powers that he has to learn to control quickly to face a new and powerful enemy.