One possible plot twist could be that Naruto discovers a new power source that makes being a Jinchuuriki seem obsolete. Maybe he finds an ancient artifact or a new form of chakra that is more powerful and doesn't have the drawbacks of being a Jinchuuriki. Another could be that he has a moral dilemma about the nature of the Jinchuuriki system and decides to quit in protest. For example, if he realizes that the Jinchuuriki are being used as tools more than protectors.
Well, perhaps Naruto quits being a Jinchuuriki because he wants to break free from the cycle of pain associated with it. He has seen how the other Jinchuuriki have suffered, like Gaara. He might think that by giving up this status, he can start a new life without the constant threat of the tailed beast inside him going berserk. It could also be that he meets someone who shows him a different path, a path that doesn't involve being a Jinchuuriki and he decides to follow it.
One possible plot twist could be that Naruto and Hinata have to quickly learn to control their newfound Jinchuuriki powers. Maybe they are suddenly thrust into a situation where an ancient evil is awakened and only their combined Jinchuuriki abilities can stop it. For example, they might discover that there is a hidden prophecy about two Jinchuuriki working together to save the world.
The storyline would be completely different. Naruto's character development would take a new turn. He would no longer have the instant boost of power from the Nine - Tails. This might make him more vulnerable, but also force him to rely more on his own skills and training. His interactions with the other Jinchuuriki would also change. They might view him as a traitor to their kind or as a pioneer for a new way of living without the tailed beasts.
A plot twist might involve the other villages' reactions. When they find out Naruto is the jinchuuriki of two bijuu, they could either see him as a greater threat or try to ally with Konoha. Maybe some villages would send spies or assassins to either capture Naruto or steal the power of the bijuu from him. This would create a lot of political intrigue and danger for Naruto and his friends.
One possible plot twist could be that Naruto, as the Ten - Tails Jinchuuriki, has a hard time controlling the power at first. He might accidentally cause destruction in the Hidden Leaf Village. His friends would initially be afraid of him, but then they realize they need to help him master this power. For example, Sasuke could use his Sharingan to help Naruto understand the chakra flow better.
Perhaps the story shows Naruto exploring different aspects of the ninja world that are not related to jinchuuriki. He could be delving into ancient ninja techniques or solving mysteries that have nothing to do with the tailed beasts inside him. It might also highlight his relationships with other characters in a new light, like his rivalry with Sasuke in a non - jinchuuriki - related context.
It could also be due to personal growth. Naruto might have outgrown the ideals and limitations of being a Konoha ninja. He may have developed his own set of values that no longer align with the village's ninja system. For example, he could have found that the constant focus on missions and loyalty to the village overshadowed the importance of individual freedom and justice on a broader scale.
In this fanfiction, the plot could revolve around Naruto and the Jinchuuriki family being hunted by a powerful organization. They are forced to go on the run and hide in different parts of the ninja world. During this time, Naruto discovers more about their shared heritage as Jinchuuriki. They also have to deal with the internal struggles of some Jinchuuriki who are not fully accepting of their role, and Naruto has to use his leadership skills to keep them together and safe.
Well, the story might revolve around the brother's different upbringings. Naruto grew up in Konoha, but his brother could have been raised elsewhere. This difference in environment could lead to different views on being a jinchuuriki. For example, Naruto might see it as a way to protect the village, while his brother could see it as a curse at first. As the story progresses, they could learn from each other's perspectives and grow stronger together.
One possible plot twist could be that Rin's adoption of Naruto leads to him learning unique jutsu from her early on. Maybe she has some secret knowledge passed down in her family that she imparts to Naruto, which gives him an edge over his peers in the ninja academy.
One possible plot twist could be that the ANBU who raise Naruto secretly train him in forbidden jutsu. This would set Naruto on a path that's different from the original story. He might face more opposition from the village elders who discover this, but it could also make him a more formidable ninja earlier on.