There's also the possibility that the antagonist is a corrupted version of Naruto himself from a different time. Maybe due to the events that happened in that timeline, Naruto turned evil and now wants to stop his present - day self from changing the past in a way that would undo his own power and status in that alternate timeline.
It could be a future version of an existing villain who has also found a way to time - travel. For example, a more powerful and cunning Orochimaru from a future timeline where he has mastered even more dark jutsu. He might try to stop Naruto from changing the past in ways that would prevent his own rise to power.
Perhaps the main antagonist is a time - traveler from another dimension who has come to the Naruto universe through the time travel orb. This character could have motives that are completely alien to the ninjas, like harvesting chakra from different time periods to power their own dimension. They would see Naruto as an obstacle to their plan.
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.
It could be Orochimaru. Even in the academy days, he was already plotting and scheming. If Naruto time - travels back, Orochimaru might see him as a threat to his early plans and target him. Orochimaru's thirst for power and knowledge makes him a great antagonist for this scenario.
A time - traveling pirate who has his own agenda and wants to change the course of pirate history for his own gain could be the antagonist. This pirate might be jealous of Luffy's future achievements and try to stop him from ever becoming the Pirate King by changing things in the past.
The Riddler could be a great main antagonist. He could use his knowledge of time paradoxes and puzzles to try and outwit Batman as he travels through time. He might set up elaborate traps across different time periods that Batman has to solve.
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.
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.
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.
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.
Another possible main character could be Kakashi. He has a lot of knowledge and experience. In a 'naruto time orb fanfic', he could be the one guiding Naruto or Sasuke in their use of the time orb, or he might even be tempted to use it himself to change some past events that haunt him, like the loss of his comrades.