One possible plot twist could be that Naruto's Mokuton abilities attract the attention of Orochimaru. He might try to capture Naruto to study his unique power. Since Tsunade raised Naruto, she would be extremely protective and engage in a fierce battle with Orochimaru to keep Naruto safe. This would not only test Tsunade's strength but also Naruto's growth under her care.
One possible plot twist could be that Naruto develops a different fighting style. Since Tsunade is strong in physical combat and medical ninjutsu, and Jiraiya is a master of various ninjutsu and toad summons, Naruto might combine their teachings in unique ways. For example, he could use medical ninjutsu to enhance his own physical abilities during combat, similar to how Tsunade uses her strength. Another plot twist could be in his relationships. With Tsunade and Jiraiya as his guardians, he might have a different attitude towards the Hidden Leaf Village's elders. He could be more critical or more understanding depending on how they've influenced him. Also, his training might be more focused on stealth and intelligence gathering, skills that Jiraiya was good at, rather than just brute strength.
A possible plot could be that Naruto, under the care of Tsunade and Jiraiya, discovers new aspects of his heritage. Tsunade might know some secrets about the Uzumaki clan that she shares with Naruto. Jiraiya, being his godfather - like figure, helps him explore these new revelations. Meanwhile, the Akatsuki could still be a threat, and Naruto, with his new skills and knowledge, has to fight against them to protect the village and his loved ones.
Well, it could be that Naruto's relationship with the other Konoha ninjas changes drastically. They might see him as an outcast because of his association with Kisame. On the other hand, Naruto might try to bridge the gap between Konoha and the Akatsuki due to his upbringing by Kisame. This would create a whole new set of conflicts and alliances within the Naruto universe.
One possible plot twist could be that Naruto develops a much darker and more ruthless side due to Zabuza's influence. Instead of the optimistic and friendly Naruto we know, he might be more solitary and calculating in his approach to battles and relationships. For example, he could be more willing to use underhanded tactics like Zabuza's use of hidden mist jutsu to ambush opponents.
One possible plot twist could be that Naruto inherits Hashirama's unique Wood Style jutsu much earlier and in a more powerful form. Since Hashirama was a master of this powerful ability, he might train Naruto intensively in it. This would make Naruto stand out even more in the ninja world and perhaps change the way his peers and enemies view him.
One possible plot twist could be that Naruto gains unique fire - related powers from the phoenix. Since the phoenix is often associated with fire in many mythologies, Naruto might be able to control a different kind of fire jutsu, which would set him apart from his normal abilities in the original Naruto story.
Perhaps Naruto's relationship with the other ninja in Konoha is affected. Since Yoruichi has a different set of values and skills compared to the traditional Konoha ninja, Naruto could be seen as an outlier. This could lead to some initial misunderstandings and later, a new form of respect from his peers as they see the effectiveness of his unique upbringing.
A plot twist could be that Naruto discovers a secret about Tsunade that she has been hiding all along. It could be something related to her family or a power she has been suppressing. This discovery could either strengthen their relationship or create a rift between them. Also, there could be a twist where an outside force tries to use their relationship to gain power in the ninja world. They might try to manipulate Naruto or Tsunade to their advantage.
Naruto's character development would be greatly influenced by Tsunade's tough love. His Mokuton power would be honed not just for fighting but also for the betterment of the village. He would grow up with a sense of duty that is more in line with Tsunade's view of leadership. He might also be more reserved in showing his emotions, as Tsunade is not one to be overly emotional in public. This would be a contrast to the Naruto we know, but still retain his core of never - giving - up.
A plot twist could be that Koharu has a connection to an ancient and powerful jutsu that she passes on to Naruto. However, this jutsu comes with a dark side or a price. Naruto then has to struggle with using this power for good while also dealing with the negative consequences it brings. He might have to make some difficult moral choices that test his character in ways he hasn't been tested before.