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.
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.
There could also be a powerful, corrupt magical creature as the antagonist. This creature might have some grudge against humans in general or specifically against Harry and Ginny because of their past actions. It could use its magic to make them disappear and keep them trapped in its domain.
The main antagonist might be a corrupted Ministry of Magic official. They freeze Harry in time to prevent him from exposing their wrongdoings. This official could be working with some dark forces secretly. They might try to keep Harry frozen while they gain more power and influence in the wizarding world. Hermione and Ron would then have to fight against the Ministry's resources to free Harry and expose the truth.
It could be a dark wizard who also has some form of time - related power. Maybe he wants to use time to his advantage to take over the wizarding world. For instance, he could go back in time to eliminate the founders of Hogwarts so that he can rewrite the rules of magic for his own evil purposes.
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.
One great Harry Potter Ginny Weasley time travel fanfiction is 'Back to the Beginning'. It has Ginny traveling back in time and trying to change some of the events that happened in the wizarding world. The way she interacts with the younger versions of the characters, especially Harry, is really interesting.
Perhaps a long - lost relative of the Potter family who feels they were unjustly excluded from inheriting the manor. This relative could be jealous of Harry's status and the wealth associated with the manor. They might use dark magic to try and claim what they think is rightfully theirs, leading to a battle of magic and loyalty within the Potter family and among Harry's friends.
One possible antagonist could be a dark wizard from the past who somehow catches wind of Albus Severus' time - traveling and decides to use his knowledge of the future for his own evil purposes. Maybe a forgotten Death Eater who was thought to be dead but actually survived in hiding and now sees this as an opportunity to rise again.