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.
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.
One possible plot twist could be that Naruto discovers a long - lost Uzumaki sealing technique that has the power to either seal away a great evil or unlock a hidden power within himself. Another could be that he has to use his sealing skills to save his friends from a powerful enemy who is immune to normal attacks but vulnerable to sealing. Maybe he also finds out that his family's past with the Uzumaki sealing arts is tied to a prophecy that he is destined to fulfill through his sealing mastery.
A really interesting plot could be Naruto traveling back in time to the era before he was born. He could meet his parents and other important figures in the village's history. This would give him a chance to understand the roots of the village better and also learn some new jutsu or strategies that he could bring back to his own time to make the Hidden Leaf even stronger as a Hokage.
Another plotline could be that Naruto discovers he has a connection to an ancient and powerful clan that was thought to be extinct. This new connection could bring him new allies, new jutsu, and a whole new set of challenges as he tries to balance his loyalty to Konoha with his newfound heritage.