Perhaps they travel to a time in the past where a powerful and dangerous jutsu was first created. They have to stop the jutsu from being misused in the future. Along the way, they face challenges like dealing with the original creator who might not want to give up on his creation, and also face other ninja who want to steal the jutsu for their own evil purposes.
One plot idea could be Naruto traveling back in time and using his god - like powers to prevent the Uchiha massacre. He could secretly train Sasuke from a young age, using his future knowledge and enhanced abilities. Another idea is that he travels to the time of the Sage of Six Paths and learns even more powerful jutsu, then returns to his own time to face a new, greater threat with his new - found skills.
Maybe they time travel to a point where a major battle was lost in the past. Kakashi and Team 7 could change the outcome of that battle. For example, if they go back to the battle against the Nine - Tailed Fox when it first attacked Konoha. They might be able to prevent some of the destruction and save more lives. Or they could travel to a time when a powerful ninja was wrongly exiled, and they work to clear that ninja's name and change the course of history.
One idea could be that Team Konohamaru travels back to the time of the First Hokage. They could witness the founding of Konoha and get involved in some of the early battles against rival clans. Maybe they help Hashirama in some way and learn valuable lessons about leadership and unity from him.
In a team Iron Man time travel fanfiction, a great plot could be that Iron Man travels to the future by accident. There, he discovers a world in ruins because of some actions he took in his present. So, he has to travel back and correct those actions. He teams up with his past self and other Avengers from different time periods to make sure the future is saved. This would involve a lot of character development as the different versions of Iron Man and the Avengers have to work together and understand each other's perspectives.
They could travel to the past and accidentally change something that has a huge impact on the present. For example, Naruto might prevent an event that was crucial for the development of a certain jutsu. This would then lead to a series of challenges as they try to fix the timeline.
One idea could be that Team 7 goes back to the time of the founding of their village. They could meet the original founders and learn about the true origins of their ninja way. Another could be that they go back to a time when a great war was about to start and they use their future knowledge to try and prevent it. Or perhaps they go back to a time when a powerful and evil ninja was first emerging and they work to stop his rise to power.
One plot idea could be Harry using his time - controlling power to go back and prevent Voldemort from ever rising to power in the first place. He could change key events in the past that led to Voldemort's ascension, like ensuring that Tom Riddle never opened the Chamber of Secrets or that he didn't get the job at Hogwarts. Another idea is that Harry travels forward in time to see the future of the wizarding world and then comes back to make changes in the present to avoid a disastrous future, such as a war between different magical races. A third plot could involve Harry getting stuck in a time loop, and he has to figure out how to break it while also using his knowledge of the repeated events to his advantage, like saving his friends from a danger that he now knows will occur multiple times.
One possible plot idea could be Finn using his god - like powers to save Ooo from a new and powerful dark force. Maybe he has to sacrifice something precious in the process, like his friendship with Jake for a short time to fully unlock his powers.
One idea could be Naruto obtaining Samehada in a unique way and it enhancing his already godlike powers. For example, he might find it during a mission in a hidden underwater cave. Another plot could involve Naruto using Samehada to fight against a new and extremely powerful enemy. The sword's ability to absorb chakra could give Naruto an edge in battles.
One plot idea could be that Naruto and Naruko, with their godlike powers, have to face an ancient evil that threatens to destroy the ninja world. They use their unique abilities, like Naruto's super - enhanced Rasengan and Naruko's incredible speed and strength, to battle the foe. Maybe they also discover new jutsus along the way that are only possible because of their godlike status.