Perhaps an unknown ninja from a far - off land that the future has not been able to deal with. This ninja could have powers that are beyond what the current ninja world in Naruto's time can comprehend. He might be after some powerful artifact or knowledge that only Naruto can help protect or find in the future.
Another possibility is a future version of Madara who has found a way to break free from the seal or reincarnation cycle in a new and more dangerous way. He could be bent on reshaping the future world according to his own dark vision, and Naruto has to stop him to preserve the future.
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.
There's also the possibility that the main antagonist is an outside force from another dimension or a powerful entity that was awakened in the future. This entity might see the ninja world as a threat or simply want to conquer it for its own gain. Naruto would need to figure out how to defeat this unknown and powerful foe during his time in the future.
Cell could still be a great antagonist. Imagine a scenario where in the fanfiction, Cell follows Future Trunks through time. He then starts to absorb different beings in the new timeline in a more devious way than in the original story.
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.
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.
Maybe it's a new character. Someone who is jealous of Naruto's legacy and wants to erase it. This character could be from a hidden clan that has been in the shadows all this time. They see Naruto as a threat to their own plans for domination, so they start causing chaos in the future Naruto witnesses.
It could be a rogue shinobi who was once a student of one of the great ninja masters but turned to the dark side due to some past injustice. This shinobi could have developed a new and powerful jutsu that makes him a formidable foe for the new generation of heroes.
Danzo could be a great antagonist. If Kakashi travels back in time, Danzo's underhanded plans, like his control over Root and his desire for power, would still be in motion. He'd likely oppose Kakashi's attempts to change things for the better, especially if it threatened his own influence.
It could be Orochimaru from an earlier time. Since he was always after power and secrets, Naruto's knowledge of the Rasen Shuriken and his time - traveling abilities would be a huge threat to Orochimaru's plans. Orochimaru might try to steal Naruto's jutsu or use him to gain more power.
Danzo could be a great antagonist. If Naruto travels back in time, Danzo's schemes and thirst for power would still be there. He might see Naruto as a threat to his plans of controlling Konoha and try to eliminate him. His underhanded methods and shadowy operations would make him a formidable foe for Naruto, especially when Naruto is trying to change the past for the better.
One potential main antagonist could be an older, power - hungry shinobi who has infiltrated the Anbu in the past. This shinobi could be jealous of Naruto's sudden rise in the Anbu (due to his future knowledge) and sees him as a threat. He then starts to plot against Naruto and the Anbu's new - found positive direction. Or perhaps it's a corrupt politician in the village who uses the Anbu as a tool and doesn't want Naruto to change the Anbu's loyalty from him to the village as a whole.