It could be a rogue dark wizard who has a personal grudge against Fleur. He might see Harry as an obstacle in his path to harm Fleur. So he captures Harry and tortures him, thinking that it will stop Harry from interfering with his evil intentions towards Fleur.
Perhaps a group of dark creatures that are under the control of a more powerful being. They are sent to capture Fleur but Harry gets in the way. So they torture Harry in an attempt to make him lead them to Fleur or to just get rid of him as a threat.
In this fanfic, it might be that Fleur has been wrongly accused of a crime by a powerful magical authority. Harry tries to defend her but is captured instead. The authority tortures Harry to force him to give up on Fleur. However, Harry refuses. He endures the physical and mental pain of the torture. His perseverance might inspire some of the other characters to see the truth. Eventually, they join forces with Harry and they manage to expose the real culprit and save Fleur.
Voldemort could be the antagonist. He might find out that Harry needs Fleur to live and try to capture or kill Fleur to get at Harry. Since Harry is a threat to his power, eliminating the person Harry depends on for his life would be a strategic move for Voldemort.
Voldemort's remaining followers could be the antagonists. Even though Voldemort is gone, there are still some Death Eaters who are bitter about their loss. They might see Harry leaving with Fleur as an opportunity to get revenge on Harry or to use Fleur as a hostage to gain power. They could try to ambush them on their journey, creating a lot of dangerous situations for Harry and Fleur.
Voldemort could be a likely main antagonist. He's the most powerful dark wizard in the Harry Potter series. He might see the Avengers as a threat to his plans of total domination, not understanding their world but still seeing their power. So, he could use his dark magic to torture them, trying to break their will before eliminating them.
There could be an ancient evil spirit that has a vendetta against griffins. When it senses that Cousland has befriended a griffin, it targets them both, trying to destroy their new - found bond and cause chaos in the world they inhabit.
It could be a dark wizard who sees Harry's new prosthetics as a source of power. Maybe this dark wizard wants to steal the magic or technology behind the prosthetics to use for his own evil purposes. For example, he might believe that the prosthetic eye holds a special power that could help him see into the future or find hidden treasures.
The antagonist could be a jealous Slytherin student. They might see Harry's new snake as a threat to their own status in Slytherin house. So they try to steal the snake or harm it in some way.
It could be Draco Malfoy. Maybe he somehow manages to use a new spell or a dark object to turn Harry into a ferret out of spite. He might then try to keep Harry in that form to humiliate him in front of the whole school.
A dark entity from another dimension could be the main antagonist. It senses Anna's new powers and wants to use them to open a portal between dimensions so that it can bring its army of monsters into Anna's world. So it constantly hunts Anna down, trying to either force her to use her powers for its own evil plan or simply kill her and take the powers for itself.
It could be a rival from X Sans' past. Someone who has always been jealous of X Sans' power or popularity in the fanfic world. This character might have finally found a way to get revenge by brainwashing him.