Cell could be a great antagonist. Imagine Goten travels back in time to before Cell was complete. Cell could sense Goten's power and try to absorb him to become even more powerful. This would put Goten in a tough situation where he has to avoid Cell while also trying not to disrupt the timeline too much.
Frieza is another option. If Goten travels to a time when Frieza was still ruling the universe, Frieza would see Goten as a threat. He might send all his forces after Goten, and Goten would have to use his knowledge of future techniques to survive and also figure out a way to stop Frieza's tyranny without changing history too drastically.
It could be a time - traveling villain who is trying to disrupt the timeline for their own gain. This villain might be trying to erase certain events or people from history to change the future in a way that benefits them.
It could be a time - traveling sorcerer who wants to change history for his own evil purposes and sees Achilles as a threat. The sorcerer might try to stop Achilles from getting back to his own time or use his knowledge of the future to his advantage against Achilles.
A time - traveling bounty hunter could be the main antagonist. He might be after Lucy because she has somehow disrupted the time - space continuum. He's cold - hearted and will stop at nothing to bring her to some time - traveling justice.
Perhaps an ancient evil that was sealed away long ago but is released due to Temari's time - traveling disruptions. This evil entity then starts causing chaos in the past, and Temari is the only one who can stop it with her modern skills and knowledge.
It could be a time - traveling villain from the future who wants to change the past to gain more power in their own time. They might try to stop Naruino from achieving their time - travel goals.
The main antagonist could be a virus that has infected the game's time - travel mechanism. This virus is spreading chaos throughout different time periods in the game world. It's trying to erase certain characters or events from history, and Ralph has to stop it. The virus could take on different forms in different time periods, making it very difficult for Ralph to combat.
A new, time - traveling villain could be introduced. This villain could be from a different dimension where time works differently. He comes to Ninjago to steal its time - related artifacts to power his own dimension. His unfamiliar powers and motives would make him an interesting and unpredictable antagonist.
Perhaps an alien race that has mastered time travel long before humans. They see Earth as a target for conquest, and they use time travel to disrupt history and weaken the planet's defenses. Peggy would have to figure out their plans and find a way to stop them. This would introduce an interesting sci - fi element to the fanfiction, with Peggy having to deal with advanced alien technology and culture.
It could be a dark wizard from the past who has the power to manipulate time. This wizard might see Natsu and Mira as threats to his plans to change the past for his own evil gains. He would try to stop them from interfering with his time - related schemes.
Dr. Wily would be a very likely main antagonist. He could be using time travel to his advantage, for example, going back in time to steal important technology before Dr. Light discovers it. This would give him an even greater edge in his evil plans in the present or future.