Well, there could be new secrets revealed about the Hall of Prophecy. Maybe a young wizard stumbles upon a prophecy that was lost for centuries and has to figure out what to do with it.
It could be a young, unknown wizard who has a special gift for sensing mysteries. He or she might be drawn to the Department of Mysteries like a moth to a flame.
The most obvious torturers would be the Death Eaters. They are Voldemort's loyal followers and would do anything to please their master. If they got the chance to torture Harry in the Department of Mysteries, they would surely take it. They might want to break Harry's spirit and prove their loyalty to Voldemort.
Neville Longbottom could be a great character in Department of Mysteries fanfiction. He has grown so much throughout the original series, and his courage could be put to the test in the mysterious and dangerous Department. He could be exploring the Department in search of a plant or potion ingredient that is said to be hidden there. Ginny Weasley is also a popular choice. Her strong - willed nature and her own magical abilities would make her a formidable character in any story set in the Department. She might be trying to prove herself or uncover a mystery that is relevant to her family or Hogwarts.
One interesting storyline could be about a new mystery uncovered within the Department of Mysteries that the original characters didn't encounter. For example, a hidden chamber filled with ancient magic that has the potential to either save or destroy the wizarding world. Another could be a story where a character gets trapped in a time - loop within the Department, reliving the same events over and over until they figure out how to break free. There could also be a fanfiction where a young, unknown wizard or witch is secretly working in the Department and discovers a plot against Hogwarts by a group of dark wizards who are using the Department's resources.
Perhaps in the fanfic, Harry is lured into a trap in the Department of Mysteries. Once there, Death Eaters could torture him to find out how he was able to resist Voldemort's attempts to possess him. They might also be interested in the connection between Harry's mind and Voldemort's, thinking that by torturing Harry they can gain some sort of power over that connection.
It could show their relationship growing stronger. For example, in the dangerous and mysterious Department of Mysteries, Harry might rely on Ginny's quick thinking and courage more than ever. This could make him see her in a new light and deepen his feelings for her.
One possible plot twist could be that while exploring the Department of Mysteries, Harry and Ginny discover a hidden prophecy related not just to Harry but also to Ginny. This prophecy might reveal that Ginny has a crucial role to play in the final battle against Voldemort that no one had anticipated before.
Well, just based on that title alone, it's difficult to determine its quality. There are so many aspects that make a Harry Potter fanfic great. For example, it could explore new relationships between the characters, or create exciting new magical adventures. But we don't know if 'skull is harry potter fanfic' does any of those things. So, it might be good, it might not.