Another plot twist could be that the Akatsuki, instead of being the main antagonists, are actually being controlled by a much more powerful and hidden enemy. Naruto then has to team up with some of the Akatsuki members to fight against this common foe. This would turn the whole dynamic of the story on its head, as Naruto would have to put aside his previous grudges and work with those he once considered enemies.
One interesting plot twist could be that Naruto discovers he has a long - lost sibling from a different village. This would completely change his perception of his family and his place in the ninja world.
One interesting plot twist could be that when Naruto and Mito time travel, they accidentally change a major event in the Uzumaki clan's history. For example, they prevent the destruction of a powerful Uzumaki artifact that was originally lost. This could then lead to a whole new power dynamic in the Naruto universe, as other villages might try to steal or ally with the Uzumaki clan for this newfound power.
One popular plot twist could be Mito Uzumaki traveling back in time and accidentally changing the events that led to the Uzumaki clan's downfall. This could create a whole new set of challenges and opportunities for the characters in the Naruto universe.
One possible plot twist could be that the 'Uzumaki' who kidnaps Naruto is actually an impostor. Maybe it's someone with shape - shifting abilities who wants to use Naruto for some dark purpose. For example, they could be trying to extract the Nine - Tails' chakra from Naruto in a more brutal way than the Akatsuki ever planned.
Another plot twist might be that Kushina Uzumaki has a secret power that she's been hiding, and Naruto Uchiha is the only one who can help her fully unlock it. However, unlocking this power comes with a great cost that they both have to face together.
One idea could be exploring Naruto's deeper connection to the Uzumaki clan's sealing jutsu. Maybe he discovers an ancient Uzumaki scroll that contains a powerful sealing technique that was lost over time. This could lead him on a journey to master it and in the process, he uncovers more about his clan's history and secrets.
One idea could be that Tayuya, who was an enemy before, is now a part of the Uzumaki clan. She and Naruto discover they have a connection through their clan heritage. This could lead to them going on a journey to explore the secrets of the Uzumaki clan together.
One interesting plot twist could be that Naruto discovers he has a long - lost sibling from another village. This would completely change the dynamics of his relationships and his understanding of his own family. Another could be that Sasuke turns out to be the key to a new and powerful jutsu that was sealed away long ago, forcing Naruto to team up with him in a whole new way.
One interesting plot twist could be that Naruto discovers he has a hidden power from a long - lost clan that changes the course of the final battle. This power might be something that gives him an edge against a seemingly unbeatable foe.
A great plot twist could be that Naruto turns out to be a half - vampire. It would completely change his character arc and how others in the Naruto world perceive him.
A possible plot twist could be that Naruto's blindness was actually caused by an enemy's secret jutsu that was meant to be permanent, but it turns out that Naruto's Uzumaki bloodline has a hidden ability that can reverse the blindness under certain conditions. This would add an element of mystery and hope to the story.