One idea could be Boruto traveling back to the era of the First Hokage. He could witness the founding of Konoha and interact with the original founders. Maybe he tries to prevent a certain event that he knows will have long - term negative consequences in his own time.
A more personal plot could be Boruto traveling back to a time when his father, Naruto, was a young boy. He could see Naruto's struggles and hardships up close and gain a new understanding and respect for him. He might also try to help Naruto in some small ways without revealing his true identity, like leaving behind some useful ninja tools or giving him advice in a disguised way.
Another plot could involve Boruto and his friends traveling back to a time when a great war was about to start. They could use their knowledge of future ninja techniques to change the course of the war, but also face the challenge of not changing history too much as it might erase their own existence. For example, they might try to save a key figure who was supposed to die in the original timeline.
Another plot idea could be a crossover within the Bloodstained Arc world. For example, two groups or characters that have never interacted before are forced to team up against a new, powerful enemy. This could lead to interesting character dynamics and development.
Another interesting plot could be about a new villain that is a combination of the powers of all the previous villains in Naruto and Boruto. The characters would have to team up in new and unexpected ways to defeat this powerful foe. For example, Naruto and Boruto might have to combine their Rasengan and Vanishing Rasengan in a completely new way.
A possible plot could involve a time - travel situation. Boruto and Mitsuki get sent back in time to the era of the First Hokage. There, they have to adapt to the different ninja world of that time. They meet the young versions of their ancestors and get involved in events that could change the future. This would test their knowledge of ninja history and their skills as they try to find a way back to their own time without disrupting the past too much.
It could be a time - traveling rogue ninja from the future who has his own plans to change history for his own benefit. He might want to take over the ninja world in the past so that he can rule in the future without any opposition.
The Boruto manga time travel arc is filled with interesting elements. For example, seeing the younger versions of familiar characters and the way Boruto and co. have to be careful not to change history too much. The plot develops with a sense of urgency as they race against time to fix potential problems they've caused.
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.
One idea could be exploring a different backstory for Pain. Maybe he had a secret friendship with a Konoha ninja before turning to his dark path. This could add a new layer of complexity to his character and the conflict in the arc.
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.