Maybe it's an ancient dark wizard who was sealed away long ago but is accidentally released during Harry's second try at things. This wizard could have powers and motives that are completely different from Voldemort's, and pose a whole new set of challenges for Harry and his friends.
Another possibility is a corrupt member of the Ministry of Magic. They could be using their power to suppress magic users, especially Muggle - borns, and Harry and his friends have to oppose this new form of tyranny instead of just Voldemort.
It could be a rogue Death Eater who decides to carry on Voldemort's legacy in a more extreme way. This Death Eater might have some new and terrifying dark magic up their sleeve.
It could be a power - hungry Death Eater who didn't like how Voldemort was running things and decides to take over after his defeat. This character might be even more cruel and calculating than Voldemort, using dark magic in new and terrifying ways.
A group of rogue Death Eaters could be the main antagonists. They think that Voldemort has gone soft by teaming up with Harry. So they break away and form their own more extreme and violent group. They start attacking both the wizarding world and anyone associated with Harry and Voldemort's new alliance. Harry and Voldemort must then fight against their former allies who have become a greater threat than ever.
It could be a dark fairy who is jealous of the Fairy King's alliance with the wizarding world. This dark fairy wants to destroy the connection and take over both the fairy realm and the wizarding world.
Perhaps it's a corrupted Hogwarts professor. In this fanfiction, a teacher could have been influenced by the dark side and decides to oppose Harry's new path. They could be using their position at Hogwarts to spread dark magic teachings or to manipulate students against Harry. They would be a more insidious antagonist as they are operating from within the very institution that is supposed to be a safe haven for Harry.
It could be a rogue Death Eater who wants to take over Voldemort's position and sees Harry and Bellatrix's new - found alliance as a threat. For example, a Death Eater who was always jealous of Bellatrix's closeness to Voldemort.
The main antagonist could be Dumbledore. Since Harry has joined Voldemort, Dumbledore would see Harry as a threat to the good of the wizarding world. Dumbledore would try to bring Harry back to the right side, and they would end up in conflict.
It could be a distant relative of Voldemort who has been biding their time in the shadows. They might have a vendetta against the Potter family for what happened to Voldemort. This relative could be secretly gathering followers and planning to strike at the second child when they least expect it.
It could be a follower of the God of Death who misinterprets the God's will and tries to bring chaos to the wizarding world. They might see Harry as an obstacle to their plans and try to eliminate him.
It could be a new dark wizard or witch who rises to power. Maybe someone who was once in Voldemort's shadow but now sees an opportunity with Voldemort gone (in this new fanfiction scenario where Snape has a second chance). This character could oppose Snape's attempts to reform the wizarding world and bring about a new era of peace and magic.
It could be a new dark wizard who has been secretly building his power. Maybe this wizard uses the allure of the cane and the idea of a new kind of dark magic to draw Harry in. He might be a former follower of Voldemort who has his own plans for domination and sees Harry as a useful tool.