One common theme is the idea of betrayal. Naruto feels betrayed by Konoha in some way, like if they hid secrets about his family or misused his power. Another theme is corruption. Fanfictions often depict Konoha's leadership as corrupt, which leads Naruto to plot against them.
Well, it could be due to corruption within Konoha. If Naruto witnesses high - ranking officials abusing their power or making decisions that harm the innocent, he might decide to rebel. He's always been about protecting the weak and standing up for what's right. And if Konoha starts to go against those principles, Naruto would not stand idly by. It could also be that he's framed by someone in the village and then has no choice but to fight back against the false accusations and the system that allows such things to happen.
One interesting plot could be Naruto being framed by a powerful enemy within Konoha, making him seem like a traitor. So he has to fight against Konoha to clear his name. Another plot might be Naruto disagreeing with some extreme and unjust policies of Konoha's leadership and decides to oppose them. Maybe there's also a plot where Naruto is influenced by a dark power that makes him turn against Konoha at first but then he struggles to break free and find a way to reconcile.
Gaara could be one of the characters. He has a bond with Naruto and if Naruto is against Konoha, Gaara might get involved to help Naruto or at least try to mediate. Shikamaru is another likely character. His intelligence would make him a key figure in trying to understand Naruto's motives and also in devising strategies for Konoha. Hinata might be involved as well, because of her feelings for Naruto. She might try to protect Naruto from Konoha's attacks.
A certain fanfiction has Naruto believing that Konoha is using him and his friends as mere tools for their own political gain. So, he starts to secretly plan against Konoha. He forms alliances with some outcast shinobi. This fanfiction explores what would happen if Naruto's loyalty was completely broken, which is a very different take from the original story where Naruto is a symbol of loyalty to Konoha.
The village would likely be in shock at first. Naruto is a hero to many in Konoha. So, some would immediately try to reason with him, believing that there must be a misunderstanding. The ninja council would probably be divided. Some would see Naruto as a threat and want to take him down immediately, while others might advocate for a more diplomatic approach to find out his motives.
Well, in some fanfictions, Naruto might outsmart Konoha by using his unique knowledge of the village's secrets that others don't know. For example, he could use his understanding of the old tunnels under Konoha to his advantage in a situation where he needs to escape or gain an upper hand in a conflict.
Well, one possible plot could be that Naruto discovers some dark secrets about Konoha's past, like how they mistreated his family. So he decides to take revenge. He might start by gathering allies outside of Konoha, perhaps some rogue ninjas who also have a grudge against the village. Then, he could use his powerful jutsu to infiltrate Konoha and expose those secrets to the public, causing chaos within the village.
Naruto's character would develop in a way that shows his growth from a wronged individual to a force of change. Initially, his revenge - driven self would be single - minded. However, as he interacts with different people during his quest for revenge, he might learn new things about Konoha's history and the reasons behind some of the actions that made him angry. This new knowledge could make him more empathetic. He could end up not just seeking revenge but also working towards a solution that benefits both himself and the village, which would be a major shift in his character.