A possible plot could be that in the 'naruto time travel academy fanfic', Naruto goes back and discovers a hidden conspiracy within the academy that was overlooked in the original timeline. He then teams up with his younger self (sort of a mind -meld situation) and some of his friends to expose the conspiracy and save the academy from an unseen threat. This would involve a lot of sneaking around, using his future knowledge of the academy's layout and the people in it.
One interesting plot could be the main character going back in time and using modern knowledge to change the outcome of some key battles in the Naruto universe. For example, they could introduce new jutsu combinations or strategies.
One idea could be that the time travel orb sends Naruto to a crucial point in the past where he can prevent a major tragedy. For example, he might be able to stop the Uchiha massacre, which would change the entire future of the ninja world. This would lead to different alliances and power dynamics.
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.
Another plot could be that they time - travel to a point where a powerful enemy is about to attack Konoha. Naruto and Mikoto form an unlikely duo. Naruto's ability to inspire and Mikoto's Uchiha powers combine to create a unique defense strategy. Along the way, they might also discover secrets about their own families and the history of the ninja world that were previously unknown.
Perhaps Ichigo could travel to a future version of the academy that has been taken over by a powerful enemy. He then has to find a way to go back in time and prevent this from happening in the first place. He could also learn new powers in this future academy that he brings back with him to his own time.
One idea could be Batman traveling back to the time when Gotham was first founded. He could try to prevent the seeds of corruption from being sown. Another plot could be him traveling to a future Gotham that has been completely overrun by villains and he has to find a way to change that future by altering events in the past. Or perhaps he travels to different time periods to gather knowledge and technology to better fight crime in his own time.
In a Naruto and Tsunade time travel fanfic, they might travel to a time when the Uchiha clan was at its peak. Naruto could try to prevent some of the tragedies that befell the clan later. Tsunade, with her strength and wisdom, could help in diplomatic efforts. For example, she could work with the clan leaders to improve relations between the Uchiha and the rest of the village. This would not only change the future for the Uchiha but also for Naruto's own life as he has a deep connection with Sasuke, an Uchiha. And Naruto could learn new jutsu from the powerful Uchiha of that time, further enhancing his own skills.
A cool plot for a Pokemon time travel fanfic might be that a Pokemon researcher travels back in time to study ancient Pokemon species that are now extinct. Along the way, they encounter problems like not being able to use modern technology to catch or study the Pokemon. They might have to rely on the knowledge of the people in that era. Also, a trainer could travel through time to meet their ancestors who were also Pokemon trainers and learn about their family's history in the Pokemon world.
One idea could be that Luffy travels back to the time when Gol D. Roger was still alive. He could meet the Pirate King and learn some of his secrets. Maybe Roger gives him a hint about the One Piece that changes Luffy's understanding of his journey.
Maybe a character from the future RWBY world travels back to the time when the Huntsman academies were first founded. They could introduce new fighting techniques or ideas that were developed in their time, which would have a huge impact on how the early Hunters and Huntresses are trained.