The Akatsuki members could also take on more extreme and evil roles. They were already antagonists in the original, but in a very dark fanfic, they could be even more cruel and have more devious plans, constantly thwarting Naruto and pushing him towards a darker path.
It could be an evil version of Sasuke. In the original story, Sasuke had his dark moments, and in a very dark fanfic, he could be fully consumed by evil and oppose Naruto in a much more malevolent way.
The Hidden Leaf Village itself could be an antagonist. If Naruto goes evil, the village that once was his home would be against him now.
The other shinobi villages might also be antagonists. If Naruto's village is seen as a threat because of his power, they could target him. This would make Naruto angry as he's being attacked for no good reason other than fear. Their actions against him and his village could lead him to a darker state as he has to fight back against these external threats.
The main character is Naruto. In the past, he will surely encounter his parents. Minato and Kushina would be important characters in this fanfic. Also, Jiraiya, his mentor, would be a key figure. Since Naruto is going to the past, he might seek Jiraiya's guidance even more. And characters like Orochimaru would also be part of the story as Naruto may try to stop Orochimaru's evil plans earlier.
Obviously, Naruto and Orochimaru are the main characters. Naruto is the protagonist who is going to Orochimaru, and Orochimaru is the one Naruto is going to see.
In a world where Naruto is a fish out of water, the local bullies or those who uphold the unfair traditions of the world could be the antagonists. They might oppose Naruto when he tries to change things for the better.
Perhaps some of the jealous monster students who don't want Naruto to succeed in school could be antagonists.
It could be some powerful demon lords in hell. They might see Naruto as an intruder and try to stop him from whatever his goal is.
Obviously, Koyuki herself would be a main character to interact with Naruto. She might show him around her place, introduce him to her people. Also, any of her loyal guards or advisors could interact with Naruto. They could be initially suspicious of him but then grow to trust him as they see his good intentions.
The main antagonists could be the original Naruto's friends and allies. Since this is an evil Naruto, people like Sasuke, Sakura, and Kakashi would likely oppose him and try to stop him from whatever evil plans he has in the past.
Well, Naruto is a given. Then there could be other minor gods or spirits in Kami's realm that Naruto meets. Maybe there's a guardian spirit of the ninja world that only appears when someone tries to reach Kami. Also, characters like Kakashi could be involved. He might have some knowledge about Kami that he imparts to Naruto before the journey, or he could even end up joining Naruto on his adventure to Kami.