Maybe she discovers a hidden prophecy that states she has the power to either destroy Voldemort or become his most powerful ally. This would create a great internal struggle for her as she was raised by him but also has a sense of good. She might start to manipulate Voldemort into making decisions that would eventually lead to his downfall.
One plot twist could be that Hermione discovers she has a hidden connection to the Malfoy family, like she's a long - lost relative. This would add a whole new layer to her being raised by them. Another could be that she uses her knowledge of both the Gryffindor and Malfoy ways to broker peace between the two factions in the wizarding world that are often at odds. Maybe she uncovers a secret plot within the Malfoy family that goes against her new - found loyalty to them, forcing her to choose between her upbringing and what she believes is right.
One interesting plot twist could be that the Kitsune endows Naruto with unique fox - like powers that are different from his normal chakra. For example, he might be able to communicate with other fox - related spirits in the forest. Another twist could be that the Kitsune's upbringing makes Naruto more in tune with nature, so he has an easier time learning certain types of jutsu related to the elements. And perhaps, due to the Kitsune's influence, Naruto has a different view on the concept of family, leading to some interesting interactions with his friends who have more traditional family structures.
One common plot twist is that Hermione discovers her heritage at a crucial moment, like when she's about to be attacked by Death Eaters and suddenly some hidden power related to her being Voldemort's heir emerges. Another is that she has to struggle with the moral implications of being related to such an evil figure.
One interesting plot twist could be Hermione struggling with her dark heritage while trying to uphold her Gryffindor values. Maybe she discovers a hidden power within her that she initially fears is evil but later uses for good.
In certain fanfictions, a plot twist is that Harry doesn't kill Voldemort directly. Instead, he uses his love and friendship magic in a very unique way. He manages to make Voldemort see the error of his ways, and Voldemort sacrifices himself to undo all the evil he has done. This is a very different take from the usual 'kill or be killed' scenario. Another interesting plot twist could be that the killing of Voldemort reveals a long - hidden prophecy about Harry that has nothing to do with the original prophecy, and this new prophecy sets Harry on a whole new path of discovery and adventure.
One interesting plot twist could be that Harry Potter has to sacrifice his own magic to defeat Voldemort completely. In this scenario, after the final battle, Harry becomes an ordinary wizard - no more special powers. But he is okay with it as he has saved the wizarding world.
One interesting plot twist could be that Kami's magic is so different from the wizarding world's that Harry develops entirely new spells. For example, he might be able to use nature - based magic in ways wizards never thought of. Another could be that Kami's values of honor and purity influence Harry to take a different stance on the fight against Voldemort, perhaps trying to redeem him first. Also, the magical creatures in Kami's world could interact with the ones in Harry's world in unexpected ways, like a friendly competition between a hippogriff and a kirin.
One interesting plot twist could be that the animals teach Naruto unique jutsu that are based on their natural abilities. For example, the birds could teach him a flying jutsu that no human has ever mastered before. Another twist might be that Naruto discovers he can communicate with all animals, not just the ones that raised him, which gives him an edge in battles and in gathering intelligence.
Perhaps there's a fanfiction where Hermione disguises herself as one of Voldemort's supporters to infiltrate their ranks. She has to be extremely careful not to be discovered as she tries to find a way to stop a major plot they are hatching. Along the way, she discovers the complex reasons some people became supporters and uses that knowledge to her advantage.
One possible plot twist could be that Hermione discovers a hidden power within herself that is not in the original books. For example, she might find out she has a special connection to an ancient magic that only warriors possess. This could change her role in the wizarding world completely and lead her on a new adventure to master this power.