One possible ally could be Yamato. He has knowledge of the Wood Release and could help Naruto better understand and control his new power. Shikamaru might also become an ally. He is smart enough to see through the false accusations against Naruto. And there are the Akatsuki members who might have a change of heart. For example, Itachi's spirit could guide Naruto in some way, or Kisame could see Naruto's potential and side with him.
Naruto's allies could include some of the forest spirits if his Wood Release has a connection to them. Also, the orphans or the lower - class ninjas in Konoha who feel betrayed by the village's decision to banish Naruto could join him. There could be a group of rogue ninjas who have their own reasons to oppose Konoha's unjust actions and they team up with Naruto, seeing him as a symbol of hope against the corrupt system in the village.
Well, the plot could involve Naruto being wrongly accused of something major, leading to his banishment. With his newfound ability of Wood Release, perhaps he teams up with some outcasts. He might use the Wood Release to create a new home for himself and his new allies, and then seek to prove his innocence to Konoha while also protecting his new place from any threats.
Naruto could potentially be allied with those who oppose the traditional power structure of the ninja world, not just limited to specific villages. There might be a group of ninja who believe in a more equal and just ninja world without the dominance of the big five villages. He could also form an alliance with some mysterious and powerful individuals who have their own agendas and see Naruto as a useful tool outside of the Konoha context.
If Naruto is banished to the My Hero Academia universe, Deku could be his ally. Deku, with his determination to be a hero, would understand Naruto's drive to be recognized. They could share their experiences of being underestimated at first. Also, in a crossover with the Inuyasha world, Kagome could be an ally. She has a kind heart and could help Naruto understand the new world he's in. Her spiritual powers might also interact in an interesting way with Naruto's chakra.
Perhaps Danzo could be the main antagonist. He was always a bit of a shadowy figure in the original Naruto series. In this fanfic, he might see Naruto and Sasuke as a threat to his own control over Konoha. So, he uses his influence to have them banished. He could be secretly working with external forces to further his own agenda while keeping Naruto and Sasuke away from Konoha.
Sasuke could be one of his allies. Despite their past differences, Sasuke might see Naruto's new path as a way to create a better world. He could offer his combat skills and strategic mind to help Naruto rule. Another ally could be Hinata. She has always been supportive of Naruto, and as emperor, Naruto would need someone he can trust, and Hinata fits that role perfectly.
Sasuke could be an ally. He also has his own issues with Konoha and would understand Naruto's need for revenge. They could combine their powers, with Naruto's massive chakra reserves and Sasuke's unique Sharingan abilities.
One possible plot could be that Naruto and Sasuke are wrongly accused of a serious crime against Konoha. For example, they might be framed for conspiring with an enemy village. As a result, they are banished. Naruto, with his unwavering spirit, might start thinking about how to prove their innocence from outside the village. Sasuke, on the other hand, could initially be more bitter and focused on getting revenge on those who framed them. Together, they embark on a journey to find the real culprits while also facing various challenges outside Konoha, such as dealing with other ninja clans who see them as outcasts and potential threats.
Sasuke could be an ally. Despite their past differences, Sasuke might see the injustice of Naruto's banishment and decide to join him. He could bring his powerful Sharingan skills to the new village. Also, some of Naruto's old friends like Shikamaru or Choji might secretly support him and provide resources or information. They could be like undercover allies still within the old village but helping Naruto's new village in various ways.
Maybe a group of rogue ninjas who initially see Naruto as a target but then end up joining forces with him. They have different skills and personalities that add to the story.
It could be a hidden group within Konoha that was behind Naruto's banishment. They might be afraid of his growing power and influence. This group could work in the shadows to stop Naruto from ever returning to Konoha and regaining his status.