Perhaps an entity from a different dimension that is using Narukaka's time travel as a way to enter and take over the world. This entity could be manipulating Narukaka without them realizing it, setting up various traps and obstacles along their time - traveling journey.
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.
An ancient sea devil who was sealed away in the past but is awakened by their time - traveling. This devil could have the power to manipulate time itself and tries to stop Luffy and Nami from returning to their own time or achieving their goals.
Voldemort could still be the main antagonist. Even if they travel back in time, his evil plans and his thirst for power would still be a major threat. He might sense something is amiss with Narcissa's behavior if she starts to act against him, and of course, he would see Harry as a huge threat regardless of the time period.
Another could be a time - traveling Pokémon hunter. In the future, Pokémon might be extremely rare, and this hunter travels back in time to capture as many as possible. Ash and Serena would have to stop him to protect the Pokémon of the past and preserve the future they know. He could be really powerful with advanced future - tech to capture Pokémon.
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 a time - traveling villain who wants to change the past to suit their own evil purposes. Maybe they want to stop Jaune from ever becoming a hero so they can rule the future world unopposed.
It could be a future version of Team Rocket. They might have become more powerful and devious in the future and travel back in time to stop Ash from achieving something important in the past that would prevent their future rise to power. Another option could be a time - traveling Pokemon hunter who wants to capture rare and powerful Pokemon from different time periods, and Ash stands in his way.