It could also be due to Naruto's outcast status in the village initially. Danzo might think that banishing Naruto would be an easy decision as Naruto doesn't have many supporters at first. He might believe that by getting rid of Naruto, he can maintain the status quo in the village and prevent any disruptions that Naruto's presence might cause in the future.
Naruto might be initially shocked and heartbroken. He has always considered the village his home, despite how some of the villagers have treated him. So being banished would be a huge blow to him.
Perhaps in this fanfiction, Yugito was involved in a political intrigue within the Hidden Cloud Village. Naruto, being an outsider with influence, banished her to maintain peace between different factions. Yugito's actions or associations might have been such that it was the only way Naruto saw to prevent a civil war or major conflict in the village.
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 motive could be to gain control over Naruto's power. Since Naruto has the Nine - Tails within him, Danzo might want to use that power for his own political or military gains. He's always been power - hungry and sees Naruto as a tool to achieve his goals of making Konoha stronger in his own way, which might involve more underhanded and controlling methods.
It could also be a completely new character introduced into the fanfiction. A foreign ninja who was inspired by some of Danzo's ideas (not the bad ones) and comes to Konoha to take on the role of successor, bringing in new perspectives and ways of doing things.
Well, one possibility could be that Naruto grows up with Danzo's strict and secretive ways. He might be trained in more underhanded ninja techniques. But at the same time, he could inherit Danzo's sense of loyalty to the village, though in a more extreme form. Maybe he'd struggle to balance the dark side of Danzo's teachings with his own desire for friendship and acceptance, which was a big part of his character in the original series.
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 could be that Danzo, seeing Naruto's potential, decides to take him under his wing secretly. He could train Naruto in more underhanded and strategic ways compared to the normal ninja training. Naruto might initially resist but then start to see the value in learning different perspectives of being a ninja.
A fanfic plot where Danzo gives Naruto Sharingan could start with a life - or - death situation. Danzo sees Naruto as the only hope and gives him the Sharingan to give him an edge. Naruto then has to quickly adapt to the new power. As he does, he starts to have visions related to the Uchiha's past through the Sharingan. These visions lead him on a quest to uncover the truth about the Uchiha massacre and Danzo's role in it. This could lead to a conflict within the village as Naruto uncovers dark secrets and has to decide what to do with the knowledge and his new - found power.
Well, it could be that Danzo trains Naruto in some ancient and forbidden jutsu. Naruto, being the curious and determined character he is, is intrigued by these new powers. However, he soon discovers that these jutsu come with a price. He has to struggle with the moral implications of using such powerful and potentially dangerous techniques while also trying to keep his identity as a jinchuriki a secret. This would create a lot of internal conflict for Naruto and also change his relationship with Danzo throughout the fanfic.