It could be a time - traveling dark wizard from an even further back era. This wizard might have his own plans for the wizarding world that conflict with what Harry and Narcissa are trying to achieve. He could be extremely powerful and have knowledge of magic that is long forgotten in Harry and Narcissa's time, making him a formidable foe.
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 option is that the antagonist is an ancient magical being that has been awakened by Harry Peverell's time - traveling disruptions. This being, which was once in a slumber, now sees Harry as an intruder in the timeline and wants to restore the order of things by getting rid of him. It could have powers that are not well - known in the modern wizarding world, making it a very difficult enemy to defeat.
It could be an ancient dark wizard who was trapped in a time - locked state but is now released due to the time - traveling disruptions caused by Harry and Teddy. This wizard might see them as threats to his own dark designs on the wizarding world and try to eliminate them.
It could be a dark wizard from the past who senses Teddy's anachronistic presence and tries to use his time - traveling knowledge for evil. Maybe a wizard who was on the verge of creating a really dark magic but was stopped in the original timeline, and now with Teddy's interference, he gets a second chance.
It could be a dark wizard from the past who somehow senses that Harry and Teddy don't belong in that time and tries to use their presence for his own evil gains. Maybe he wants to steal their future knowledge to become even more powerful.
Voldemort could still be the antagonist even if they travel back in time. If they go back to a time when he was already active, like when he was at Hogwarts as Tom Riddle, he could oppose their attempts to change the future or disrupt his plans. He might sense their presence and try to eliminate them.
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.