One possible reason could be that he's framed for a dark magic crime he didn't commit. Maybe a powerful dark wizard manages to plant false evidence on him. Another reason might be a misinterpretation of his actions. For example, if he uses a powerful spell in self - defense but it's misconstrued as an offensive and illegal spell.
In some fanfictions, it could be due to political intrigue within the wizarding world. There might be a faction that wants to get rid of Harry Potter as he's seen as a threat to their power. So they manipulate the situation and get him sent to Azkaban. Also, it could be related to a prophecy that certain people want to prevent from coming true, and they think imprisoning Harry is the way to do it.
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.
One possible storyline could be Harry's struggle to prove his innocence while in Azkaban. Maybe he discovers some dark secrets within the prison walls that are related to a larger threat to the wizarding world. Another could be his attempts to escape and the friends he makes or enemies he encounters during the process.
One reason could be the aftermath of his battles. For example, the physical and mental scars from fighting Voldemort. He might be in pain from the Cruciatus Curse that some dark wizards in the fanfiction might use on him. Another reason could be the loss of his loved ones. Losing Sirius, Dumbledore, and others could cause him deep emotional pain that manifests in the fanfiction as a constant ache.
One reason could be a reaction to the Ministry of Magic's mismanagement. In the original story, the Ministry often made mistakes and had corrupt elements. In fanfiction, this could lead to Harry becoming an anarchist as a way to oppose such a flawed system.
One reason could be to add more depth to his character. Schizophrenia can bring out complex emotions and behaviors, making Harry more relatable in some ways.
It could be a case of misinformation. Someone in the story might have spread false rumors about Harry being the father for their own motives. Perhaps they wanted to cause chaos or gain something from the situation. So, the whole idea of Harry being the father is just a false story that gets spread around the wizarding community.
One reason could be to give him a stronger connection to Hogwarts. As the heir, he might have special privileges or knowledge about the school. Another reason is to add a new dimension to his character. It makes him more than just a student who defeated Voldemort.
One reason could be for creative exploration. Writers may want to see how the story changes when the main character has an androgynous appearance.
Another possible reason is that Harry is protective of their story. Fanfiction can be quite wild with different interpretations, and he might not like how some fanfictions try to rewrite their relationship. He has a deep - seated understanding of his bond with Hermione, and fanfiction that messes with that can be hard for him to tolerate. He might think that the real story is already great and doesn't need these made - up alterations.
One possible reason could be to gain extraordinary powers. In some fanfictions, giving up humanity might be a sacrifice for a greater magical ability, like being able to control all elements or access a new level of magic that is otherwise inaccessible to humans.