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.
Another idea is that Harry has to face Voldemort in a new way. Since he is a Dragonborn, he can call upon dragons to aid him in the battle. The dragons could be used to attack Death Eaters or to create a distraction while Harry uses his combined wizard and Dragonborn skills to finally defeat Voldemort. Maybe the dragons are attracted to the powerful magic that Voldemort wields and see it as a threat to their territory.
A third plot idea is that fem Harry Potter is actually a long - lost relative of Loki in some convoluted way. This discovery leads to a series of events where they have to work together to uncover the truth about their shared heritage. Along the way, they face opposition from both the wizarding community who fear her newfound connection and some Asgardians who don't trust an outsider.
One idea could be Naruto using his time - control ability to go back in time and prevent the Uchiha massacre. This would completely change the course of the Naruto universe, leading to different alliances and power dynamics. For example, Sasuke might not have the same drive for revenge, and the Akatsuki's plans would be disrupted as Itachi would not be a rogue ninja.
In some fanfictions, Harry controlling time might lead to him altering his own past. He could change how he was treated by the Dursleys. Maybe he goes back and uses magic to make them more accepting of him from the start, which would have a huge impact on his character development and his relationship with magic in his early years.
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 idea could be Harry going back in time to his parents' era at Hogwarts. He could try to prevent certain events that led to their deaths. Another could be him going back to the time of the founders of Hogwarts and getting involved in the creation of the houses and Hogwarts' early rules.
One idea could be that Finn and Jake from Adventure Time end up in the wizarding world of Harry Potter. They could use their unique abilities to help Harry and his friends in a dangerous quest, like finding a hidden Horcrux. Finn's sword could be useful against dark magic creatures, and Jake's shape - shifting might come in handy for sneaking around Hogwarts.
One idea could be that a time - twisting spell goes wrong and Harry ends up in the past during the founding of Hogwarts. He has to navigate the very different magical society then while trying not to change the future too much. Another could be that Voldemort discovers a time - twister spell and uses it to try and change the outcome of his battles with Harry. Or perhaps Hermione accidentally activates a time - twister device and she and Harry have to fix the timeline that gets all jumbled up.
One interesting plot could be the main character using time - traveling magic from the Harry Potter world to change key events in the Lord of the Time's story. For example, they might go back to prevent a certain dark wizard from obtaining a powerful time - related artifact.
One idea could be that Harry and Ginny travel back in time to the Marauders' era. They could interact with James, Sirius, Remus and Peter, and perhaps change some small events that later have a big impact on the fight against Voldemort. For example, they could give the Marauders some tips on how to better hide from Snape, which in turn could make Snape less bitter in the future.