There could be an adventure where a new threat emerges that combines the worst of both their worlds. For example, an enemy that can use both chakra - like powers and has the ability to mimic some of Ben's alien forms. Naruto and Ben would have to quickly figure out the enemy's weaknesses. They could travel to different places, from the forests of Konoha to the deserts of Ben's home planet. Along the journey, they would learn more about each other's powers and grow closer as brothers. They might also meet some old friends or foes from their respective universes, adding more complexity and excitement to their adventure.
They could have adventures where they explore different dimensions. Naruto's ability to travel through his world could be combined with Ben's inter - galactic travels using the Omnitrix. They might end up in a dimension full of strange creatures and have to fight their way out together.