One possible plotline could be that when sent back, they try to change the future by preventing certain tragedies. For example, they might work to stop the death of some of their friends.
Perhaps they are sent back with some special knowledge or abilities. They could use this to their advantage in the past, like Hermione using her future - learned magic to solve problems that were previously difficult. They might also try to change the way they interacted with other characters in the past to improve relationships and outcomes.
It could be Voldemort still. Even if Harry and Hermione are sent back in time, Voldemort would still be a major threat. His dark magic and his followers could oppose Harry and Hermione's attempts to change things.
One interesting plotline could be Naruto using his future knowledge to prevent the Uchiha massacre. He might be able to change things in a way that doesn't lead to Sasuke's downward spiral. Another could be him training his younger self to be stronger faster, so that he can face the early threats in the Naruto world more effectively.
One interesting plotline could be Naruto using his future knowledge to prevent certain tragedies. For example, he might stop the Uchiha massacre by warning the clan or finding a way to resolve the conflict between them and the village earlier. Another could be him training his younger self more effectively, leading to a much stronger Naruto at an earlier age. He could also change the way he interacts with characters like Sasuke, maybe preventing Sasuke from leaving the village in the first place.
Some fanfictions explore a different relationship dynamic between them. Maybe Harry has a problem that only Hermione can understand and help him with, and this brings them closer in a way that's different from their normal friendship. It could be something related to his connection with Voldemort or his family history.
In some fanfictions, their training might involve time - traveling. Maybe they go back in time to learn from the founders of Hogwarts. Harry could learn how to better control his connection to Voldemort through this time - traveling training, and Hermione could study ancient magic from the founders. This would add a whole new dimension to their skills and knowledge.
One possible plotline could be Hermione using her intelligence to create a stable and loving home environment for Harry. Maybe she helps him deal with his PTSD from his past traumas. Another could be them facing magical threats together as a family, with Hermione teaching Harry new spells and ways to protect himself.
One interesting plotline could be Harry and Hermione discovering a long - lost secret vault in Gringotts. Maybe it contains powerful magical artifacts that can change the course of the wizarding war. Another could be that they are on a mission to retrieve something from the vault that is crucial for their fight against Voldemort, like a spellbook with ancient and powerful spells.
One possible plotline could be that they are practicing magic for an upcoming difficult exam at Hogwarts. They might be working on advanced spells like the Patronus charm and Hermione is helping Harry perfect it.
One possible plotline could be that they escape from a dark wizard's lair. Maybe they use their combined magic skills and Hermione's extensive knowledge to find a secret passage out. Another could be escaping from a dangerous magical creature's territory by using clever spells and potions.
Perhaps a plot where they all become animagi and have to use their animal forms to solve a mystery in the Forbidden Forest. Draco as a sleek snake, Harry as a stag, and Hermione as an otter, they must navigate the forest's dangers and uncover the truth about a strange magical disturbance.