A possible plot twist could be that Danzo reveals a hidden power related to the Sharingan that no one knew about. Maybe he can combine the powers of all the Sharingan he has in a unique way that gives him an edge over Naruto.
If we consider a Naruto - Danzo fight in a fanfiction, Naruto has several factors in his favor. His training with Jiraiya and other experiences have made him a formidable ninja. He can go into Sage Mode, which enhances his physical abilities and gives him access to more powerful jutsu. Danzo, while being a shrewd and experienced ninja, has his weaknesses. His over - reliance on the Sharingan and his somewhat underhanded methods might not be enough against Naruto's raw power and unwavering spirit.
Another aspect could be that the successor discovers some long - hidden secrets left by Danzo. These secrets could be related to powerful jutsu or ancient ninja lore. And as they uncover these secrets, they have to decide whether to use them for the good of the village or keep them buried to avoid causing chaos.
Well, one possible plot could be Naruto growing up under Danzo's influence. He might be trained in more underhanded and secretive shinobi techniques. For example, he could be taught to prioritize the village's security above all else, even if it means using morally gray methods. This would put him at odds with some of his friends who follow more traditional ninja values.
One possible plot could be that Danzo, despite his controversial nature in the original Naruto series, sees potential in Naruto. He might train Naruto in the ways of stealth and intelligence gathering. This could lead to Naruto having a more diverse skill set, different from what he learned from Jiraiya. Maybe Danzo would teach Naruto some of the Root's unique jutsu, which Naruto could then adapt to his own style, making him an even more formidable ninja.
Well, perhaps Danzo kidnaps Naruto because he sees Naruto as a threat to his secretive and often unethical operations. He might fear that Naruto will eventually expose his wrongdoings. So, he takes Naruto to a hidden location and tries to keep him there, but Naruto's friends like Sasuke and Sakura would then start a rescue mission.
The plot could involve Danzo falling in love with a female jonin. He might initially hide his feelings as he is a very private person. But as they are assigned on a mission together, they start to bond. He could be attracted to her combat skills and her strong will.
One possible plot could be that Naruto, with his godlike powers, is able to see the good intentions behind Danzo's actions that were previously misconstrued. He then works with Danzo to bring about a new era of peace in the ninja world. Danzo, with Naruto's influence, starts to use his resources and influence for the greater good instead of his own political gain.
One possible plot could be Naruto developing new and unexpected powers as a result of the experiments. Maybe he has to struggle to control these new abilities while also dealing with his feelings of betrayal towards the village that allowed Danzo to do this to him.
The plot could involve Naruto having a philosophical discussion with Danzo. Naruto, with his idealistic views of peace and friendship, might try to sway Danzo from his more ruthless ways. They could talk about power, sacrifice, and what it really means to be a shinobi. Naruto could also demand answers from Danzo about the secrets he's been hiding from the village.
One possible plot could be that Naruto is somehow transported to a different timeline where he has to fight the Hokage for a misunderstanding. Maybe there's a villain who has manipulated events to make the Hokage think Naruto is a threat. So Naruto has to fight not only to prove his innocence but also to save the village from the real danger that the villain poses.