Well, perhaps a big plot twist would be in the romance area. As a girl, Naruto could attract different suitors. This might create jealousy among some of the male characters who were previously just his friends or rivals. His understanding of the opposite sex could change completely, and he might use his new perspective to his advantage in missions, like being able to infiltrate places more easily as a female. Another aspect could be that his fighting style might be adjusted to suit a more feminine physique while still maintaining his powerful ninja skills.
A possible plot twist could be related to her powers. If Percy had certain powers before, they could be altered or enhanced in unexpected ways after reincarnation into a girl. For instance, her physical strength might be combined with a new kind of magical ability that is unique to female characters in that fictional universe. Also, there could be a twist where she discovers a hidden connection to a female - only group or prophecy that she was unaware of as Percy. This could lead her on a whole new adventure and change the direction of the story.
One possible plot twist could be that Naruto, now in Yugi's body, tries to use his ninja skills in the world of Duel Monsters. Since he has no prior knowledge of the game, his attempts to blend in and use his own combat - like approach to dueling would be really interesting. For example, he might try to physically attack the opponent's monsters instead of using cards in the proper way at first.
One possible plot twist could be that Naruto, as a girl, has to infiltrate an all - female organization. He might struggle with the different social dynamics and expectations of being a girl in that context. For example, he could be expected to act more demurely, which would be a big change from his normal boisterous self.
A plot twist could be that a curse or a magic spell is cast on Naruto that makes him slowly turn into a girl against his will. He then has to find a way to reverse it while dealing with the emotional and physical changes. Along the way, he might learn some valuable lessons about gender identity and the importance of self - acceptance. He could also find that some of his enemies treat him differently as a girl, which gives him an advantage in some battles and a disadvantage in others.
One possible plot twist could be that Orochimaru turns Naruto into a girl as part of a grand experiment. But Naruto, now a girl, still has his (or rather her) strong will and uses this new form to infiltrate an all - female group that Orochimaru wants to target. This way, Naruto can gather intelligence and thwart Orochimaru's plans from the inside.
One interesting plot twist could be Naruto's use of chakra in the wizarding world. Since wizards use magic, Naruto's chakra-based abilities like the Rasengan could be a completely new and unheard - of power there. Another could be his take on the Hogwarts houses. With his strong sense of loyalty and friendship, he might not fit neatly into the traditional Gryffindor mold that Harry did. He could also introduce ninja - style combat to the duels at Hogwarts, which would change the dynamics of how battles are fought in the wizarding world.
In a Naruto is Vergil fanfiction, it could be that Naruto's connection to Vergil is through a dream - like realm. Every time Naruto sleeps, he enters a world where he meets Vergil and learns from him. Over time, Naruto starts to incorporate Vergil's values into his own. He becomes more focused on power for the sake of protecting those he loves in a more 'Vergil - esque' way, which means he might be willing to make some sacrifices that he wouldn't have considered before, like sacrificing some of his own personal relationships for the greater good of the village.
One possible plot twist could be Naruto's struggle to adapt to a different gender identity within the ninja world. He might face discrimination or confusion from his peers at first. For example, his male friends like Sasuke or Shikamaru might be initially shocked and not know how to act around him. However, Naruto's strong will would likely drive him to prove that gender doesn't define his abilities as a ninja. He could still pursue his dreams of becoming Hokage, but now also deal with the added challenges of being a female in a male - dominated society in the ninja world.
He could be reincarnated as one of the Uchiha clan members. This would be really interesting as he would have to deal with the Sharingan and the Uchiha's history. He might even change the fate of the clan.
One possible plot twist could be Percy's struggle to adapt to the new gender. For example, she might face challenges in how society now treats her. Maybe she was used to certain privileges as a boy that are now different. Another twist could be in her relationships. Her friends might react in various ways, some being very accepting while others are confused or even distant at first. And she could also discover new aspects of herself, like different interests or ways of expressing emotions that were suppressed before.