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 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.
It could be the Green Goblin. Since Harry has a connection to the Green Goblin in the original story, it would be interesting if the Green Goblin resurfaces in a new and more powerful form. Peter and Harry would have to put aside their differences and past traumas related to the Green Goblin to team up and defeat this common enemy.
In a 'Harry Potter and Voldemort team up' fanfiction, the plot could involve a prophecy that states only the combined power of the two can save the wizarding world from an upcoming cataclysm. At first, they are reluctant, but as the signs of the impending doom become more evident, they put aside their differences. They use their combined magic to unlock ancient secrets and find magical artifacts that are needed to prevent the disaster. This new alliance also causes a major shift in the power dynamics and relationships within the wizarding world.
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.
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 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 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 Draco Malfoy. He's always been a bit of a troublemaker for Harry. Maybe he gets his hands on a new spell or potion and decides to use it on Harry during class to embarrass him by plugging up his magic or voice.
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.