Another possibility is a corrupted version of Naruto himself. Due to some dark magic or unforeseen consequence in the time chamber, Naruto's dark side is split off and becomes a powerful antagonist. Naruto has to fight his own dark self in order to fully master his powers and come out of the chamber as a stronger and more balanced ninja.
Maybe a rogue ninja from another village who has also found a way into the time chamber. This ninja has a vendetta against Naruto and the Hidden Leaf and tries to stop Naruto from achieving his training goals, or worse, tries to use the time - warped powers of the chamber for his own evil plans.
It could be an ancient evil ninja who was sealed away long ago and somehow gets released in the time chamber. Naruto has to face this powerful foe while also dealing with the time - warped environment of the chamber.
It could be a rogue Saiyan from another part of the universe who somehow manages to enter the hyperbolic time chamber. This Saiyan might have a grudge against Gohan's family or be on a quest for power and sees Gohan as an obstacle.
A powerful demon from another dimension could be the antagonist. This demon, drawn to the energy of the Hyperbolic Time Chamber, tries to take it over. It has the ability to create illusions inside the chamber, making Goku's training even more difficult and dangerous.
Madara Uchiha could also be a main antagonist. If Naruto goes back to a time when Madara was still alive and plotting, Madara would surely oppose Naruto's attempts to change the future. He has his own grand plans for the world and wouldn't let Naruto interfere easily.
Perhaps an old enemy has returned, stronger than ever. They might have been plotting during Naruto's sealing and now are ready to take on Naruto and the Hidden Leaf Village. This could be someone like Orochimaru who found a new way to gain power in Naruto's absence.
Danzo could still be a major antagonist. Even if Naruto travels back in time, Danzo's thirst for power and his underhanded methods would still pose a threat. Naruto would have to find a way to deal with him without causing too much chaos in the village.
It could be Orochimaru. Imagine Orochimaru discovers baby Naruto's time - traveling ability and wants to use it for his own evil purposes. He might try to manipulate baby Naruto to change the timeline in a way that benefits him, like making it easier for him to gain more power or revive his dead comrades.
It could be a future version of Orochimaru who has found a way to come back even more powerful. Maybe he has developed some new form of immortality and is causing chaos in the future world that Naruto travels to.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
The Basilisk is an obvious main antagonist. It is a huge and powerful magical creature that has the ability to kill with a single glance. In the original story, Harry barely manages to defeat it. In a fanfiction where Harry dies, it could be that the Basilisk is just too strong for him to overcome.
It could be a rogue ninja who has mastered a forbidden jutsu during the time skip. This ninja might have been a former ally or a student from one of the ninja academies who turned to the dark side. His goal could be to take over all the ninja villages using the power of the forbidden jutsu.