One way could be that Naruto has been repeatedly let down by Konoha. Maybe he was mistreated in the past, like being ostracized despite his efforts to protect the village. So in the fanfiction, he decides he's had enough and stops caring.
Perhaps he discovers some dark secrets about Konoha that make him lose faith in it. For example, if he finds out that the village leaders were involved in unethical actions or were using him all along. This could lead to him not caring about Konoha in the fanfiction.
In the fanfiction, Naruto might have met people from other villages who showed him a different way of life. These new experiences and relationships could make him question his loyalty to Konoha. He could start to see that there are other places that are more accepting and less judgmental, causing him to care less about Konoha.
It could be due to some kind of misinformation. He might have been led to believe that his family didn't care about him, so in turn, he stopped caring about them. For example, if false rumors were spread about his family's intentions, it could warp his perception.
Another plot development might be that Konoha asks Naruto to train the next generation of ninjas. Naruto, being the hero of the village, has a lot of skills and knowledge to pass on. He might face challenges in training the newbies, like dealing with their different personalities and abilities, but in the end, he manages to create a strong new generation for Konoha.
One way to justify it could be through a series of betrayals. Maybe Naruto discovers that Konoha has been using him all along, and his family has some dark secrets that make him feel betrayed. For example, if he finds out that his father was involved in some unethical experiments that led to the suffering of many villagers, that could turn him against both Konoha and his family.
He could feel betrayed by the village. For instance, if they wrongly accused him of something or didn't support him when he needed it. In fanfiction, this could lead to him turning his back on Konoha. Another possibility is that he meets someone who convinces him that Konoha's values are wrong, and there are better ways to live outside of the village.
Well, in some fanfictions, it might be justified by a complex backstory. Maybe Voldemort realizes that Harry has some power or knowledge that could be useful to him in a different way than just killing him. So, instead of harming Harry, he decides to heal him to gain an advantage.
Naruto could become more self - centered. Since he no longer has the overarching goal of protecting Konoha, he might focus more on his own needs and desires. For example, he could pursue personal power or adventure without considering the implications for the village.
The fanfiction changes the relationship dynamics within the Naruto world. Usually, Konoha is at the center of Naruto's universe. But now, with Naruto not caring about it, other elements like his personal relationships outside Konoha or his own self - discovery become more prominent. It shifts the focus from the village - centered story to a more individual - centered one.
In a dark 'naruto executed by konoha fanfiction', it could be that Konoha, fearing Naruto's power, decides to execute him. Maybe they believe false rumors spread about him. It's a very tragic and dark take on the Naruto universe.
In a 'naruto conquers konoha fanfiction', perhaps Naruto could be pushed to the edge by the corrupt system in Konoha. He might decide to take over to bring real change. He could use his powerful jutsu and the loyalty of his friends to overthrow the old regime and install a more just rule.
It could also be a sparring session gone wrong. Naruto might be training with the Konoha 12, but his new and powerful techniques are too intense. This causes the others to feel threatened and they end up in a full - on fight. Naruto would then have to control his power and show his friends that he doesn't mean to harm them.