One possible plot could be that Naruto discovers he has some Uchiha blood in him. This revelation would change his perspective on himself and his place in the ninja world. He might then start to train more intensively to master Uchiha abilities.
A plot could revolve around Naruto being adopted by an Uchiha family at a young age. As a result, he grows up with Uchiha traditions and skills. He could face challenges from the rest of the village who are suspicious of his newfound Uchiha connections, but he uses his Uchiha training to prove himself and protect the village.
Perhaps in this fanfiction, Naruto being born an Uchiha means he has a natural rivalry with Sasuke from the start. Since they both have Uchiha blood, they might compete not just for power but also for the right to be the true heir of the Uchiha legacy. Also, his Uchiha lineage could attract the attention of Orochimaru, who might see Naruto as a new vessel with the potential of the Uchiha powers.
One possible plot could be Naruto having to deal with the expectations and the dark legacy of the Uchiha name. He might struggle with the power that comes with being Madara's son. For example, he could have an in - built affinity for powerful Uchiha jutsus like the Sharingan from birth, but also face prejudice from those who fear the Uchiha. Another aspect could be how his relationship with Sasuke changes. Since Sasuke is also an Uchiha, Naruto might have a different dynamic with him, perhaps a more competitive or brotherly one where they both explore their Uchiha heritage together.
The plot might also focus on her relationships. As a fem Naruto who is an Uchiha Jinjuriki, her friendships with Sasuke and others would be different. She might have a deeper connection with Sasuke as they now share the Uchiha heritage in a way. And her relationship with the other villagers would change too. Some might fear her, while others see her as a symbol of hope. She could use her powers to bridge the gap between the different factions in the village.
One possible reason could be a misunderstanding. Maybe Naruto is forced into a situation where he has to take actions that seem like a betrayal to the Uchiha. For example, if there are political forces at play that make Naruto choose between the safety of the village as a whole and the specific interests of the Uchiha clan. Naruto, being a firm believer in the village's unity, might make a choice that the Uchiha perceive as betrayal.
In this kind of fanfiction, one possible plot could be that Mikoto is in danger from an unknown enemy. Naruto, with his strong sense of justice and his powerful ninja skills, somehow discovers her plight. Maybe he stumbles upon a battle where Mikoto is outnumbered and on the verge of defeat. He then jumps into the fray, using his Rasengan or other signature moves to fend off the attackers and save her.
In a Naruto joins the Uchiha clan fanfiction, he could be adopted by an Uchiha. For example, if Sasuke had a change of heart early on and decided to bring Naruto into the clan. Naruto would then be exposed to the Uchiha's dark past and their thirst for revenge. He could use his own positive attitude to try and change the clan's perspective. And he'd surely have to train hard to keep up with the Uchiha's high standards in combat and ninja skills.
Well, a really interesting plot twist might be that Naruto's upbringing among the Uchiha makes him question his own identity more than in the original story. He might be torn between his Uzumaki heritage and the Uchiha values he was raised with. For example, the Uchiha are known for their pride and a certain sense of isolation in some ways. Naruto, with his usual sunny disposition, could either rebel against these aspects or try to find a new way to incorporate them into his life. This internal conflict could lead to some really intense character development and might even change the way he approaches his relationships with other characters like Sasuke. Maybe he'd understand Sasuke's actions from a different perspective, which could completely shift the dynamic of their relationship.
One possible plot could be that Naruto travels back in time and meets Mikoto Uchiha. He might try to prevent the Uchiha massacre. Since Naruto has knowledge of future events, he could use this to his advantage. He could also form an unlikely alliance with Mikoto, who was an important figure in the Uchiha clan. This could lead to a whole new timeline where the Uchiha clan doesn't face destruction and Sasuke has a different upbringing.
The fanfiction could explore how Naruto Uchiha's character changes as the son of Zeus. He might become more confident, yet also more burdened. His relationships with his family and friends could be completely transformed. For instance, Sasuke might see him as a threat now that he has divine heritage. And Naruto would have to prove himself not just as a ninja, but as a worthy son of Zeus, perhaps by going on a quest to retrieve a powerful artifact that is important to both the ninja and godly worlds.
The plot could involve the younger brother trying to protect Naruto. Since Naruto is female in this universe, she might be more vulnerable in some ways. The younger brother could use his Uchiha powers to fend off those who would harm her, all while dealing with the politics of the Uchiha clan.