Kakashi could also be an ally. He has a deep bond with Naruto and respects Shikamaru's intelligence. He might secretly support them, providing them with information or resources they need while they are banished. He could act as a sort of mentor from the shadows.
Gaara of the Sand Village could be an ally. Given Naruto's past relationship with Gaara and how they both understand the pain of being ostracized, Gaara would likely offer his help. He could provide a safe haven for them in the Sand Village and assist in their quest to clear their names.
Sasuke could be a likely ally. Despite their past differences, Sasuke might see the injustice in Naruto and Shikamaru's banishment and decide to help them. He has his own reasons to oppose the village's wrongdoings at times.
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.
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.
I think Hinata could be an ally. She has always been in love with Naruto and would not stand by while he is in danger from Dark Naruto. Additionally, Shikamaru is smart and strategic. He might see the threat of Dark Naruto to the village and decide to assist Naruto, using his intelligence to come up with battle plans.
The village elders could be antagonists. They might see Naruto and Kakashi as threats to their traditional way of ruling the village and use false accusations to banish them.
Rock Lee could be an ally. His determination and hard - working nature would be very useful in the rebuilding process. He could help with the physical labor of building structures. Also, some of the Uzumaki clan members who were scattered around different villages after Uzushiogakure was destroyed might come together and ally with Naruto to restore their ancestral home.
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.
Sakura and Sasuke are very likely allies. Sakura has her medical skills and combat abilities, and Sasuke, despite his past issues, has great power. They've been comrades with Naruto for a long time.
Definitely Naruto is the central figure. In the harem, Hinata is a very likely character since she has always been in love with Naruto. Sakura might also be there as she has been one of Naruto's closest friends. Tenten could be another addition. She has interacted with Naruto in the series and could potentially be part of the harem in this fanfiction. Also, Temari, who has had some interesting encounters with Naruto, might be a character in the harem as well.
There are also the wandering ninja. These are ninja who don't belong to any particular village. They might join forces with Naruto because they understand what it's like to be on the outside. Together, they could form a sort of 'rogue' ninja group.
Sakura would definitely be one of his allies. She's always been by Naruto's side, and in this fanfiction, she could help him with his disguises, like using her medical ninjutsu to create more realistic physical changes. Kakashi could also be an ally. His intelligence and experience would be valuable in planning Naruto's undercover missions. He could teach Naruto how to act more convincingly in different disguises.