One possible plot could be Naruto using the bunker as a secret training ground. He could practice new jutsus without being disturbed, and perhaps discover some hidden power within the bunker. Maybe there are ancient markings or seals in the bunker that he deciphers, leading to a new level of strength.
His relationships with his friends in the village would likely become strained. Since he's living in a bunker, he's away from them. They might worry about him and feel left out. For example, Sasuke might think Naruto is avoiding him on purpose.
Naruto might run into a group of rogue ninjas who are using the bunker as their hideout. This would lead to a confrontation where Naruto has to use his skills to defeat them and protect the village from their potential threats.
Well, Naruto might find some ancient secrets in the bunker. Maybe it's filled with old ninja tools or scrolls that hold powerful jutsu. It could also be a hiding place for a villain he's been after, leading to an epic battle.
He could also interact with the scientists on Pandora. They might be interested in Naruto's abilities and study him. Naruto could in turn learn about their technology, which is so different from what he has in his own world. He might even help them solve some problems they have on Pandora using his ninja wisdom.
It might be about Naruto living freely in a sense that he can make his own choices regarding his relationships. For example, he could choose his friends and allies more freely without political interference. In this fanfiction, he might not be bound by the traditional shinobi rules and hierarchies, allowing him to interact with different clans and villages on his own terms.
Obviously, the foxes would be the main characters. There could be an old, wise fox that acts as Naruto's mentor among them. It could have a name like Kyo, and it would be the one to teach Naruto the most important lessons.
Gaara would be an obvious choice. Since Gaara is from Suna, he could be Naruto's close friend. They could train together and share their experiences of being jinchuriki. Kankuro and Temari might also become his friends. Kankuro could teach Naruto some of his puppet techniques, and Temari could help Naruto with wind - style jutsu training.
Sasuke could be one of his companions. Even though they've had their differences, they always end up coming together for big challenges. Sasuke's sharingan would be useful on the moon, helping them detect any hidden threats. Another could be Kakashi. His experience and knowledge would be invaluable in a new and strange environment like the moon. He could also teach Naruto and Sasuke new techniques based on the moon's conditions.
In this fanfiction, perhaps Hinata and Naruto are living together and learning more about each other on a deeper level. Hinata could be teaching Naruto some of the traditional Hyuga clan techniques, while Naruto shows Hinata some of his unique jutsu. Their living situation might also involve a lot of visits from their friends like Sakura and Sasuke, creating some really fun and heart - warming group dynamics.