Perhaps a plot twist could be that the training by 'good' Danzo is a ruse set up by the Akatsuki. They want to manipulate Naruto through Danzo and lead him astray. Naruto, being perceptive during the training, realizes something is off and has to outwit both the Akatsuki and figure out Danzo's true role in this scheme.
A plot twist might be that the 'good' Danzo is actually being controlled by an even greater evil. Naruto, during his training, starts to notice strange behavior in Danzo and uncovers this conspiracy. This would lead to Naruto having to not only deal with his training but also save Danzo from this unseen force. It would add a whole new layer of complexity to the story.
One possible plot twist could be that Danzo, despite being 'good', has a hidden agenda related to Naruto's power. Maybe he wants to use Naruto to gain political influence in the Hidden Leaf. Another twist could be that Naruto discovers Danzo's past misdeeds while being trained, which creates a moral dilemma for him. He has to decide whether to continue training under someone with a dark history or break away.
In this fanfic, perhaps Naruto's godlike powers would be a result of Danzo's unorthodox training methods. Danzo could push Naruto to his limits, making him a force to be reckoned with. Naruto might also have to deal with the distrust of his friends at first, as they are suspicious of his association with Danzo.
One possible plot twist could be that Danzo's extreme methods actually lead to an unexpected period of peace in Konoha. He might suppress all forms of dissent so harshly that no one dares to start any internal conflict. But this peace comes at a cost. The villagers live in fear, and the younger generation starts to question the true meaning of being a ninja. For example, Naruto, who is used to the more open - minded leadership of others, might struggle to adapt to Danzo's regime and secretly plot to change things from within.
One possible plot twist could be that Tsunade trains Naruto not just in physical combat like she did with others, but also in medical ninjutsu. This would be unexpected as Naruto is more known for his brute force. Maybe Naruto uses his new medical skills in a creative way during a battle, like healing his opponents to show mercy and then defeating them when they are off - guard.
A plot twist could be that Slade has an ulterior motive for training Naruto. Maybe he plans to use Naruto as a weapon against Konoha in the future. He might be secretly feeding information about the village's defenses to an enemy while training Naruto. So, when Naruto discovers this, he has to find a way to stop Slade and also deal with the fact that he has been unknowingly part of a scheme against his own home.
One possible plot twist could be that Mikoto discovers Naruto has a hidden kekkei genkai that she helps him unlock. This new power could completely change Naruto's abilities and how he's perceived in the ninja world.
One possible plot twist could be that Sakumo's training methods are very unorthodox compared to what Naruto is used to in the village. For example, he might focus more on stealth and assassination skills which Naruto initially struggles with as he is more used to head - on combat. Another twist could be that Sakumo has a hidden agenda for training Naruto, like he is preparing Naruto for a specific threat that he foresees but hasn't shared with the village yet.
A plot twist could be that Urahara's training makes Naruto lose his ability to use shadow clones for a while. This forces Naruto to rely on other skills he's learned from Urahara, like swordsmanship or some new type of jutsu. It would also make his friends and enemies question his power and how to deal with this new Naruto.
One possible plot twist could be that Zabuza's training methods lead Naruto to develop a darker side. Naruto might start to question his own values as Zabuza's more ruthless ways of fighting seep into his mindset. For example, he could become more willing to use underhanded tactics in battles, which would shock his friends.
Another plot twist could be that Obito is secretly training Naruto to fight against an even greater enemy that no one else is aware of yet. This enemy could be an ancient force that is about to awaken, and Obito believes Naruto is the only one who can stop it. So, he's training Naruto in unique and unorthodox ways that seem strange to others at first.
One possible plot twist could be that Danzo is actually being controlled by an even greater enemy. So, when Naruto is about to defeat him, he realizes that there's a bigger threat behind Danzo. Another could be that Danzo reveals a hidden power that he has been suppressing all along and suddenly becomes much stronger than Naruto expected.