Maybe it turns out that Harry's connection to Merlin was hidden on purpose by a powerful wizard who feared the combined power of their bloodline. When this secret is revealed, it sets off a chain of events where Harry has to fight against this wizard and his minions who are trying to stop him from fully embracing his heritage. And all the while, he still has to deal with his normal Hogwarts challenges.
A possible plot twist could be that Merlin is not actually dead but has been trapped in a different dimension. Harry, as his son, has to find a way to free him. This would completely change the dynamic as they could then fight side by side against the forces of evil.
One plot twist could be that Harry discovers he's Merlin's son just as he's about to face Voldemort in a final battle. This new knowledge gives him a sudden boost of power and knowledge that he didn't have before. He realizes he has access to spells and magic that Merlin had created but were long forgotten. This changes the course of the battle and the outcome of the entire wizarding war.
One possible plot twist could be that Harry has hidden magical abilities passed down from Regulus that no one expected. Maybe he can communicate with certain magical creatures in a unique way.
A possible plot twist could be that Harry discovers he has an inheritance from Helga Hufflepuff that gives him the power to control certain magical creatures in a unique way. This could change his adventures in the Forbidden Forest, for instance.
One possible plot twist could be that Merlin is carrying a child with magical powers far beyond what anyone has seen. This could lead to a race among the dark forces to either control or destroy the unborn child, while Merlin's friends strive to protect him and the baby.
Well, it could be that Naruto, as Merlin's son, has hidden magical powers that he discovers gradually. Maybe he uses these powers in the Naruto universe to fight stronger enemies or to bring peace in a different way. For example, his magic could be combined with his ninja skills.
One possible plot twist could be that Naruto's primordial powers are sealed away by an unknown force, and he has to go on a journey to unlock them. Another could be that his friends turn against him when they discover his true nature as the son of a primordial being, fearing his power.
One possible plot twist could be that Snape has a hidden agenda all along. Maybe he's been using Harry as a pawn in a bigger scheme related to the wizarding world's power struggle. Another could be that Harry discovers a long - lost family connection to Snape that changes their dynamic completely.
One possible plot development could be that with Merlin's help, Harry discovers a new form of magic that was previously unknown. This new magic could then be used to defeat a powerful enemy.
A really cool plot twist in some 'Harry Potter and Morgana Merlin fanfiction' is the idea that Morgana was actually an experiment by an ancient wizard in the Harry Potter world long ago. So her presence in the Merlin universe was a sort of exile. When she returns to the Harry Potter world, she has a different perspective and new powers. Another interesting twist is that the sorting hat in Hogwarts is actually an artifact from Merlin's time, and it has a hidden connection to Morgana. This connection is revealed when a new student arrives who has a special link to both universes, and it sets off a chain of events that no one could have predicted.
Often, there's a plot twist where some magical interference or prophecy was involved in hiding the truth. Maybe a powerful wizard or witch cast a spell to make everyone believe Harry was James' son when in fact he was Snape's. And then, as the fanfiction unfolds, there are signs and clues that start to surface. Like, Snape's strange behavior towards Harry throughout the years at Hogwarts might be because he was his father but couldn't show it. It creates a really interesting re - imagining of the relationships in the 'Harry Potter' world.
One plot twist could be that Snape discovers Harry is his son right before a major battle. This new knowledge gives him the extra motivation to fight even harder to protect Harry. Another could be that Voldemort finds out about this relationship and tries to use it against them both, perhaps by threatening to harm Harry if Snape doesn't turn on Dumbledore.