Maybe some of the Akatsuki members could be his secret allies. For example, Itachi might have had a secret plan and saw Naruto's potential, so he was secretly helping Naruto become stronger all along. Also, there could be some minor characters from other villages who have recognized Naruto's hidden power and decided to ally with him.
It could be Lydia. They have a long - standing relationship in the show, and a secret marriage between them would be quite a shock. Maybe they eloped in a moment of passion and are now trying to figure out how to break the news to their friends.
Maybe some of the younger ninjas from other villages that he has inspired. For example, a young ninja from the Sand Village who saw Naruto's heroics during the Fourth Great Ninja War and now wants to join him in his quests. They could bring new skills and perspectives from their own village's ninja techniques.
An alien race that is highly intelligent but physically weak. They see Naruto as a powerful protector. In return for Naruto's protection, they offer him their advanced technology which could be crucial in his journey back to his world. For example, they might give him a device that can create wormholes to different parts of the universe.
In some fanfictions, his secret spouse could be an original character created by the author. This character might be a fellow wizard or witch who has a special connection with Snape, perhaps they met during his early years at Hogwarts or in some other part of the wizarding world. They could share a common interest in potions or some other magical art, which brought them closer.
His friends like Sasuke could be his allies. Sasuke, despite his own complex journey, has a deep connection with Naruto. He would understand Naruto's need to fight against the council if they were being unjust. Also, Sakura, with her medical skills and growing strength as a ninja, would be a great asset. She could heal the team during any confrontations and also use her combat skills when necessary.
Kirishima could be an ally. His tough exterior and unwavering loyalty would make him a great partner for Kaminari. He could protect Kaminari when he's in a vulnerable state, like when he overuses his quirk. Also, Momo could be on his side. With her intelligence and ability to create useful items, she could provide Kaminari with gadgets and strategies to succeed in his secret agent missions.
Hermione and Ron would surely be his first allies. They have always been by his side through thick and thin. Also, Luna Lovegood might be an ally. She has an open - minded and accepting nature, and she would probably see Harry as still being the same person despite his new form.
Daenerys could be an ally. Since she is the mother of dragons, she might initially be hesitant but then see the potential in Jon Snow riding one of her dragons. They could team up to fight their common enemies.
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.
Sasuke could potentially be an ally. Even though they have their differences, in the Akatsuki setting, they might realize they need to work together. Another could be Itachi. Itachi has his own motives and might see Naruto as a key to achieving certain goals within the Akatsuki. Also, Konan could be an ally. She seems to be more open - minded compared to some of the other members and might be swayed by Naruto's positive attitude.