One possible plot twist could be that the person who denies Naruto has an ulterior motive. Maybe they are being controlled by an enemy ninja who wants to keep Naruto from having power in the village. Another twist could be that Naruto discovers a hidden prophecy that says his true destiny is not to be Hokage but to lead a different kind of revolution in the ninja world.
Well, one plot twist could be that Naruto is denied Hokage because of some false accusations against him. As he tries to clear his name, he uncovers a conspiracy within the village that goes deeper than he thought. Another twist could be that the village decides to abolish the Hokage system altogether just as Naruto is about to be named Hokage. This throws Naruto into a state of confusion, but also gives him the opportunity to re - imagine what leadership in the village could be like. Also, it could be that Naruto is denied Hokage due to a mysterious power that is influencing the decision - makers, and Naruto has to find a way to break that power's hold to prove his worthiness for the role.
One possible interesting story could be Naruto facing some sort of political conspiracy within the village that leads to his hokage denial. Maybe some elders or a hidden group want someone else in power for their own motives.
One possible plot twist could be that the second Hokage had some secret enemies who target Naruto because of his lineage. Another could be that Naruto discovers some hidden jutsu or power that was passed down specifically from the second Hokage. Maybe there's a twist where the village initially rejects Naruto because they believe the second Hokage had some dark secrets that they fear Naruto might inherit.
One possible reason could be that some elders in the village still have doubts about his past. For example, his connection with the Nine - Tails. They might fear that this could lead to instability in the village. Another reason could be political intrigue. There might be other powerful clans or individuals who want the position for themselves and manipulate things behind the scenes to deny Naruto.
One possible plot twist could be that Sadime Hokage is secretly from an enemy village but has been undercover in Konoha for years. She falls in love with Naruto during her time there and has to choose between her loyalty to her original village and her newfound feelings. Another could be that Naruto discovers a hidden power within Sadime that is related to an ancient prophecy, and they must work together to prevent a great disaster.
A common plot twist in Naruto Rokudaime Hokage time travel fanfiction is that the time - traveling Hokage accidentally alters the fate of a major character. This could be someone like Naruto himself or Sasuke. By changing their past, the future of the ninja world is thrown into chaos. For example, if he prevents Naruto from getting a certain power - up in the past, it could mean that the ninja villages are not as united in the present. Or perhaps the Rokudaime Hokage's time travel causes a shift in the balance of power between the different ninja clans. This then leads to new rivalries and alliances that were not present in the original timeline.
One interesting plot twist could be that the fourth hokage didn't actually die when he sealed the nine - tails in Naruto. Instead, he was trapped in a sort of limbo within Naruto's mind and could communicate with him at crucial moments, guiding him in ways that no one else could understand.
A plot twist might be that Naruto's Kryptonian powers are linked to the tailed beasts in some strange way. Maybe his heat vision is actually a form of the Nine - Tails' chakra, or his super strength is related to the power of all the tailed beasts combined. This would create a whole new layer of mystery and power - up potential. Also, there could be a twist where Naruto's real family from Krypton shows up in the Naruto world, and they have their own agenda that conflicts with Naruto's life in the Leaf Village.
Perhaps Naruto discovers that Kisame has a family he's been protecting in secret, and this new knowledge makes Naruto see Kisame in a different light. He then tries to help Kisame reunite with his family while also dealing with the Akatsuki.
Perhaps Naruto discovers that Sheele was sent to his world by an enemy as a spy, but she has actually fallen in love with the place and the people, especially Naruto, and she has to prove her loyalty. This would create a lot of drama and tension in the story.
A possible plot twist could be that Tsuyu is secretly related to one of Naruto's enemies. Maybe she discovers this during the course of a mission and has to decide whether to side with her newfound family or continue to be Naruto's ally.