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.
There's also the possibility that an alternate version of one of their guildmates could be the antagonist. For example, a version of Gray who turned to the dark side due to some time - travel - related event. This Gray would have different motives and powers, and would be a formidable opponent for Natsu and Mira as they try to set things right.
It could be a dark mage from the past who was sealed away but gets released because of Natsu's time travel. Maybe a mage who was trying to conquer the world back then and now sees Natsu as a threat to his new plans. Another option is a time - traveling villain who is trying to change history for his own evil purposes and Natsu has to stop him.
One possible plot could be that Natsu and Mira accidentally stumble upon a magical artifact that sends them back in time. They might end up in a time when Fairy Tail was just being founded. There, they could meet the younger versions of their guildmates and have to work together to make sure the guild's history unfolds as it should, while also trying to find a way back to their own time.
It could be a time - traveling version of Zeref. He might be trying to stop Natsu from changing things in the past that could potentially lead to his own downfall in the future.
It could be Zeref. If Natsu goes back in time, Zeref might have different plans or be in a more powerful position at that time. He could be the main obstacle for Natsu to overcome, especially if Natsu is trying to change things related to the dark magic that Zeref wields.
Another option could be a dark wizard from the past who was once defeated by the founders of Fairy Tail. But Natsu's time - traveling causes some sort of ripple effect that brings this wizard back to power. He then wants to take revenge on the guild and sees Natsu as a symbol of the future that he wants to destroy.
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.
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.