There could be a group of antagonists. A secret organization that has been operating in the shadows while Naruto was away. They oppose the values of the Hidden Leaf Village and see Naruto as a major threat to their plans. So, they try to eliminate him and disrupt the peace that Naruto has been fighting to protect.
It could be a new villain who has emerged during Naruto's absence. This person might be after the power that Naruto holds or wants to destroy the Hidden Leaf Village for some unknown reason.
Maybe an old enemy that Naruto thought was defeated has somehow returned. For example, Orochimaru could have found a new way to come back and cause chaos. He might be seeking revenge on Naruto or trying to use Naruto's power for his own evil purposes.
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.
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. Since Orochimaru has always been interested in power and immortality, if Naruto goes back in time, Orochimaru might sense the change in the timeline and try to stop Naruto from changing things that could affect his future plans for power.
It could be a rogue ninja from within Konoha who doesn't want Naruto to return because he fears Naruto's growing power will disrupt his own plans for power within the village.
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.
Cell could be a great antagonist. Even if Gohan goes back in time, Cell might still find a way to exist. Maybe he adapts his plan to absorb the Androids earlier in time. Gohan would then have to face a more powerful and unpredictable Cell, who could potentially change the timeline to his own advantage.
Frieza would be a great antagonist. If Goku goes back in time to a point before Frieza was defeated, Frieza could be an even more menacing force as Goku might not have all the power - ups he had in the original timeline. He'd have to rely on his wits and basic training more.
The antagonist could be a new, self - proclaimed ninja god who wants to rule over all the villages. He sees Naruto as the only threat to his power, so he used a powerful spell to take away Naruto's godlike abilities. Konoha wants Naruto back to stop this tyrant. This antagonist might have an army of brainwashed ninja at his command.
Perhaps an old enemy from Naruto's past that was thought to be defeated but has somehow returned stronger. Maybe Orochimaru, if he has found a new way to gain power and wants to test himself against Naruto once again. He might be jealous of Naruto's popularity and the fact that he was always seen as a hero, so he uses Edo Tensei to bring Naruto back just to defeat him and prove that he is the stronger one.
A group of rogue ninja who are hunting nekoshou for their special powers could be the main antagonists. They see Naruto's newfound connection with the nekoshou as a threat and try to eliminate him and the nekoshou he is protecting.