Kakashi might also side with Naruto in this scenario. He has trained Naruto and has a deep bond with him. If Kakashi discovers that Naruto has been wronged, he could choose to follow Naruto rather than the village's orders. Additionally, Hinata might be an ally. Her love for Naruto could make her stand by his side, believing in his good nature no matter what the village says.
One possible plot could be Naruto feeling betrayed by the village. Maybe he discovers some dark secrets about the Hidden Leaf that make him question his loyalty. For example, if he finds out that the village leaders were involved in unethical experiments. So, instead of following the village's rules blindly, he goes rogue to seek his own version of justice.
Definitely the Na'vi. They are the native inhabitants of Pandora and would likely see Naruto as an ally, especially if he shows respect for their land and culture. His skills could be useful to them in their fight against any common enemies.
Perhaps some of the less powerful youkai who are often bullied could become his allies. They would see Naruto as a protector and someone who can stand up to the stronger, meaner youkai.
Jon Snow might be an ally too. He has a good heart and is used to dealing with different cultures and powers. He and Naruto could bond over their shared experiences of leadership and fighting for what's right.
The Hidden Leaf Village itself could be the main antagonist. If they turn on Naruto for no good reason, they become the force he has to fight against as a rogue ninja.
He could meet some space - faring ninjas who have adapted to the space environment. They might have unique chakra powers related to the cosmos.
Gaara could be one of his potential allies. Since they have a history together and Gaara has changed a lot, he might support Naruto. Also, the Raikage might become an ally if Naruto can prove that his intentions are good for the entire ninja world.
Another possibility is Madara Uchiha. Even if he is not fully alive in the original story, in this fanfiction, his spirit or some form of his influence could be present. He could manipulate Naruto's new evil state for his own ends, like trying to destroy the ninja world that he once had a vendetta against.
Well, one possibility is that Naruto could be betrayed by the Hidden Leaf Village. Maybe false accusations are made against him, and in his anger and disappointment, he decides to go rogue. He might then start to form his own group of outcasts who also feel wronged by the ninja system.
The other members of Team 7 like Sakura and Kakashi could also be his allies. Sakura could use her medical ninjutsu to heal any injuries Naruto and the team get in space battles. Kakashi could offer his wisdom and combat experience, guiding Naruto in this new and unfamiliar space - filled adventure.