One idea could be a member of the Bat Clan traveling back in time to prevent the death of a key ally. This would change the course of events in Gotham and create a whole new set of challenges and relationships.
One interesting plot idea could be a character from the future traveling back to the time of the clan wars and trying to prevent a certain tragic event that led to the downfall of their clan. For example, if it was a Uchiha, they might try to stop the massacre. Another idea is that the time traveler accidentally changes the course of the clan wars in a way that creates new alliances and rivalries that were not present in the original timeline. They could also introduce future jutsu or technology into the past, which would completely disrupt the balance of power during the clan wars.
In a 'Naruto Time Travel Clan Wars' fanfic, a time - traveling character could be a descendant of one of the clans involved in the wars. They go back in time with the mission to retrieve a lost clan heirloom or secret technique. Once there, they get caught up in the clan politics and battles. Their actions during this time could either make the clan stronger in the future or lead to its downfall, depending on their choices.
Batman himself is a likely candidate. Given his intelligence and determination, he might stumble upon a time - traveling device or technology while investigating some strange phenomenon. He would be driven by his need to protect Gotham, perhaps by preventing a future catastrophe that he has foreseen.
The little bat could discover a hidden cave filled with ancient bat artifacts. It then has to protect this cave from other animals who might want to take over or destroy it. This could involve making alliances with other bats and using its wits to outsmart the invaders.
Perhaps Rouge is sent to the Naruto world to retrieve a powerful artifact that has been lost there. She enlists Naruto's help as he knows the land well. As they search for the artifact, they encounter many challenges like other ninja clans who also want the artifact. Naruto's ninja skills and Rouge's acrobatic and thieving abilities combine to make a great team.
One idea could be that the bat family encounters a supernatural force that gives them new powers. For example, they might come across a magical amulet that allows them to fly without their gadgets for a short time.
One idea could be exploring the lost techniques of the Uzumaki clan. For example, a young Uzumaki descendant discovers an ancient scroll that holds the key to a powerful sealing jutsu long forgotten. This could lead to a series of adventures as they try to master it while also fending off those who want to steal the knowledge.
One idea could be exploring a hidden sub - clan within the Uchiha clan that has a unique kekkei genkai. Another could be a story about a member of the Hyuga clan who rebels against the traditional ways of the clan and tries to create a new future for it. Maybe a story where a Naruto - like character is born into a minor, almost forgotten clan and rises to great prominence.
One idea could be Yoda traveling back in time to train Anakin Skywalker differently, thus preventing his fall to the dark side. Maybe he goes back to the very beginning of the Jedi Order to gain more knowledge about the Force and bring it back to his own time.
One idea could be Shinji traveling back in time to prevent the Second Impact. He might try to change the actions of his father that led to it. Another could be Asuka traveling to a future where the Evangelions have been completely forgotten and she has to figure out how to get back to her own time.