Maybe Naruto leaves the village because he's framed for a crime he didn't commit. Disillusioned with how quickly the villagers turn against him, he decides to leave. During his time away, he uncovers a conspiracy that actually targets the village. He then has to decide whether to come back and save the people who wronged him or let the village face the consequences on its own.
In one possibility, Naruto might leave the village to seek greater power on his own. He could feel that the village's teachings and training methods are limited. So, he embarks on a journey across different lands, meeting new shinobi and learning unique jutsu that the village doesn't offer. This could lead to him coming back much stronger, but also with a different perspective on the village and its values.
Well, Naruto could leave the village in a fanfic due to a prophecy. He might believe that leaving is the only way to fulfill a greater destiny that the village can't support. As he leaves, he starts to explore different cultures of the ninja world. He learns about new forms of jutsu and how other villages operate. He could also form a team with outcasts from different villages, and together they strive to change the way the ninja world views things.
Well, one possible plot could be Naruto starting from scratch. He might first gather like - minded ninjas who share his vision of a new kind of village. Then, they'd have to find a suitable location, perhaps a place rich in natural resources but also defensible. Naruto would use his charisma and his own experiences in Konoha to create rules that are fair and inclusive. For example, he could ensure that all ninja clans, no matter how small, have a voice in village matters. And he'd probably want to establish a ninja academy that focuses not only on combat skills but also on things like diplomacy and understanding different cultures among ninjas.
Maybe Naruto is betrayed by someone within the village who sets him up to look like he's dead. Left for dead, he's found by a hermit who teaches him new and powerful jutsu. With his new skills, he plans to return to the village to expose the traitor and prove his worth once again.
One possible plot could be Naruto feeling a sense of disillusionment after the war. He might have seen so much destruction and death that he decides to leave in search of a true and lasting peace away from the Hidden Leaf. He could be on a journey to find other ways to maintain peace among the ninja clans without the use of force or political power plays.
Perhaps Naruto in the Anbu has a personal mission that goes against the village's orders. For example, he might befriend someone from an enemy village who is actually innocent but is being targeted by Konoha. When the village refuses to listen to his pleas, he decides to leave. He'll use his Anbu abilities to protect his new friend and find a new place where they can both be safe, away from the political drama of the ninja villages.
The plot could involve a character from Naruto becoming the Kage of a village other than their own. For example, Naruto could end up as the Kage in the Sand Village. This would bring a whole new set of challenges and relationships. He'd have to deal with the different political situations, the unique shinobi culture of that village, and form new alliances or rivalries. Maybe he'd introduce new training methods inspired by Konoha, which could either be welcomed or resisted by the local shinobi.
One possible plot could be that an Uchiha, perhaps Sasuke or a new Uchiha character, decides to take over the village in a more peaceful way. He uses his sharingan powers to gain the trust of the villagers by showing them visions of a prosperous future under Uchiha leadership. He then reforms the village's political system to be more inclusive of the Uchiha clan's ideas and traditions.
Well, it might be that Naruto leaves the village to search for a new power source. In the context of a yaoi fanfic, he could meet a mysterious male stranger on his journey. They start off as comrades but gradually develop deeper feelings for each other. Their relationship could be full of drama, with Naruto having to balance his feelings for this new person and his ties to his old village friends.
One major challenge would be survival. Outside the village, he no longer has the support system of the Hidden Leaf. He'd have to find food, shelter, and deal with potential attacks from other shinobi or bandits. For example, in the wild, he might struggle to find clean water and safe places to sleep.
In such a fanfic, perhaps Naruto is betrayed by his village and left in the forest. Maybe there are enemies lurking in the forest that he has to face alone. It could also involve Naruto's struggle to survive and his journey to find out why he was abandoned like this.