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.
The main antagonist could be a power - hungry elder in Temari's own village. This elder might see Temari as a threat to their authority, especially if she has been getting too much influence or support from other ninja. So, they frame her for a crime that leads to her banishment.
A power - hungry politician from one of their villages could be the main antagonist. This person might see Naruto and Temari's relationship (if that's part of the reason they are hiding) as a threat to his plans for power. He wants to use their situation to his advantage, either by forcing them to do his bidding or by getting rid of them altogether.
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.
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.
Maybe the main antagonist is a powerful figure within Konoha who doesn't want Naruto to leave and become an independent force. He secretly sends assassins after Naruto. When Temari gets involved, this figure also targets her. His actions are driven by his thirst for power and fear of Naruto's potential outside of Konoha's control.
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.