It could also be due to a misjudgment in a dangerous magical experiment. Suppose Harry was exploring some unknown and extremely risky branch of magic. His inexperience and the unpredictability of this new magic could lead to a fatal accident. He might have been too eager to learn more about magic to protect others better, but unfortunately, it cost him his life.
One possible reason could be a dark magic curse. In many fanfictions, an ancient or powerful dark magic spell might be placed on Harry, and despite all his skills and the help of his friends, he couldn't overcome it. This could be something that was secretly cast on him during his early years, perhaps related to his connection with Voldemort.
Maybe it was a heroic sacrifice. Harry was always known for his selfless nature. He might have put himself in a dangerous situation to save his friends or the entire wizarding world. For example, if there was a new and even more powerful dark wizard threatening everyone, Harry could have chosen to sacrifice himself to stop the evil, just like he was always willing to do in the original series.
One reason could be a dangerous magical accident. Maybe he was experimenting with some powerful and unknown magic that went wrong. Another could be due to a dark wizard's plot. The dark wizard might have found a way to bypass all his protections and kill him.
One reason could be a different family situation. For instance, if he was raised by someone other than the Dursleys, who might have been more involved in the dark arts. Another could be his experiences at Hogwarts. If he faced more discrimination or was wrongly accused often, it could lead to a sense of bitterness and a turn towards the dark side.
In the fanfiction, it might be that there was a powerful and unexpected dark magic curse placed on the Potter family long before Voldemort's attack. This curse was designed to target the youngest Potter, and despite the efforts of his parents, it couldn't be stopped, causing Harry to die as a baby.
Maybe he was killed by Voldemort in a more sudden and unexpected way when he was a child. Since Voldemort was always after him, it's possible that he managed to get to Harry earlier in this fanfiction.
One possible reason could be that his birth parents were in a difficult situation, like facing financial hardships or health problems. Another reason might be that they were in some kind of danger and couldn't take care of him, so they made the tough decision to give him up for adoption. It could also be that there was some sort of family secret or stigma associated with his birth that led to his adoption.
Perhaps he gets a chance to attend a special magical school or training program that requires him to leave the Dursleys. It could be a place where he can develop his powers without the Dursleys' interference. Also, he may be running away from a threat that the Dursleys are unable or unwilling to protect him from.
One possible reason could be a misunderstanding. Maybe Harry was wrongly accused of something, and Ginny's temper got the better of her. For example, if there were false rumors about Harry being unfaithful in the fanfiction world.
One possible reason could be that the 'light' in the fanfiction represents something he associates with strict rules or a false sense of goodness. Maybe it has been used to manipulate people, and Harry, being perceptive, sees through it and thus hates it.
One reason could be a powerful dark magic spell cast upon him by a new villain in the fanfiction world. This spell might be designed to make him disappear from the wizarding world entirely.
Maybe he leaves because of a conflict with the Hogwarts staff. If the new headmaster or some teachers start implementing rules that Harry believes are wrong or unfair, like restrictions on defensive magic classes, he might decide to leave in protest.