One idea could be that Merlin is reborn as a student at Hogwarts. He could use his ancient magic knowledge to solve some of the mysteries that even Dumbledore has trouble with. For example, he might be the key to understanding the true nature of the Chamber of Secrets in a way that no one has thought of before.
Another plot could involve Harry Potter being guided by Merlin reborn. Merlin, with his wisdom from a different era, could help Harry better understand his connection to Voldemort. Maybe Merlin has some insights into the ancient dark magic that Voldemort is using, and he can teach Harry how to counter it more effectively.
One idea could be that Merlin uses his magic to help Harry Potter in his fight against Voldemort. Maybe Merlin's ancient magic knowledge gives Harry an edge in finding Horcruxes. Another could be that the characters from the two universes meet at Hogwarts, like Merlin being a special guest lecturer, sharing his experiences of magic in a different era.
Well, perhaps a plot where the Eyes of Merlin are the key to unlocking an ancient prophecy that has been misinterpreted all along. This could lead to a race between the good and bad forces in the Harry Potter universe to either use it for good or evil. Also, it could be that a character who has the Eyes of Merlin has to face a series of trials to fully understand and control their power, and these trials are set up by an old wizard who once possessed the Eyes.
Well, perhaps Merlin's reborn identity as Harry Potter means he has an innate understanding of certain things. He could be able to see through Voldemort's plans more easily because he has seen similar dark wizards in his past life. Also, his relationships with the other characters like Hermione and Ron would be different. He might be a mentor - like figure to them, guiding them with his centuries - old wisdom.
One idea could be being reborn as Harry's long - lost twin. You could then have a whole new dynamic where you both share the burden of being the Boy Who Lived, but also have your own unique abilities and personalities. Another plot could be being reborn as a Slytherin who tries to change the house's reputation from the inside. You might start off being shunned by the other Gryffindors and friends of Harry, but slowly prove that not all Slytherins are bad.
One interesting plot could be a character reborn with memories of the future. For example, a minor character who remembers Voldemort's rise and fall and tries to change things in a different way. They might try to prevent certain deaths or change the course of the wizarding wars.
One idea could be a crossover where Merlin's magic system interacts with the magic of the Harry Potter world. Maybe the Reaper has some special role in uniting the two magical realms. For example, it could be a powerful entity that both Merlin and the wizards in Harry Potter's world need to face together, leading to a lot of new spells and magical discoveries.
One interesting plot idea could be that Merlin teaches Harry ancient magic that has been long forgotten in the wizarding world. This gives Harry an edge in dealing with Voldemort. Another could be that under Merlin's guidance, Harry discovers a whole new world of magical creatures that were thought to be extinct. Maybe they hold the key to defeating the dark forces. Also, Merlin could train Harry in a more holistic way of magic, not just spells and potions, but also in the spiritual and ethical aspects of magic use.
Well, a plot might involve Harry - now James - trying to change the fate of his family. He could focus on protecting Lily in a different way than James did in the original story. Maybe he'd use his knowledge of magic from his past life to create new spells or defenses. Also, his relationship with Snape could be very different. Since he was Harry before, he might understand Snape's feelings better and try to make amends or change the animosity between them.
One idea could be that Merlin somehow gets transported to the Harry Potter universe. He could use his magic, which is different from the wizarding magic in Harry Potter, to solve some of the mysteries or problems there. Maybe he teams up with Harry and helps him defeat Voldemort in a unique way, like using his ancient magic knowledge.
One interesting idea could be how the magic from Merlin's time influences the wizarding world in Harry Potter. Maybe there are ancient spells or magical artifacts passed down through Merlin's inheritance that play a crucial role in the fight against Voldemort.