The Dementors first and foremost. They don't really care about justice or innocence, and their actions are a form of torture. Then, there could be a new dark wizard or group that has emerged and wants to use Harry's situation to their advantage. They might have bribed the Azkaban staff or found a way to get in and torture Harry for their own purposes, like getting information about the Order of the Phoenix or just to create chaos in the wizarding world.
The Dementors could be the main antagonists. They are always a threat in Azkaban, sucking out the souls and happiness of the prisoners. They would be constantly trying to get at Harry and Daphne.
It could be the corrupt prison guards or wardens. They might be in league with dark forces outside Azkaban. They oppose Harry and Ginny because the couple is getting too close to uncovering their illegal activities within the prison, like smuggling dark artifacts or collaborating with Death Eaters.
Perhaps a new dark wizard or witch who has infiltrated the Ministry of Magic and made sure Harry was sent to Azkaban. This antagonist could be working towards a bigger plan to take over the wizarding world and sees Harry as a major threat even when he's locked up.
A young Auror who is assigned to help guard Azkaban but has a secret sympathy for the prisoners. This character could add a new dynamic to the story as they struggle between their duty and their conscience.
Another option is a group of demons who have a vendetta against Clary or the shadowhunters in general. They might use torture as a way to break her spirit and gain information about the shadowhunters' defenses.
It could be Sirius Black. Since he has his own experience with Azkaban, he might know some secrets about the place. He could return in some form within the fanfiction and assist Harry in his escape, maybe by leading him through some hidden tunnels or using some special skills he developed during his time in prison.
One possible plotline could be that Harry is wrongly accused and sent to Azkaban. While there, the Dementors constantly torture him with their presence, draining his happiness and hope. Another could be that a dark wizard within Azkaban has a vendetta against Harry and uses dark magic to physically and mentally torture him. Or perhaps the prison system itself, with its harsh conditions and lack of proper care, is a form of torture for Harry, and he has to find a way to endure and escape while dealing with the psychological trauma.
The Thalmor could be great antagonists. Their strict control over magic and their anti - human beliefs could put them at odds with Harry. They might see his different form of magic as a threat to their power in Skyrim.
It could be a new dark wizard who wants to make a name for himself. He sees Hogsmeade as an easy target to show his power. He starts by causing small disruptions like making objects in the shops move on their own and then escalates to more dangerous attacks that Harry has to stop.
The Death Eaters could be the antagonists. Even though Voldemort is gone, some of his followers might not want Harry to succeed in building a starship as they fear it could bring more power to Harry and his friends, and they still hold grudges against him.