One possibility is that the Dursleys, out of their extreme hatred for anything abnormal, actively sought ways to harm Harry. They might have found some dark magic item or spell that they used against him, and without the proper protection or knowledge to counter it, Harry succumbed. In the world of fanfiction, there are many dark and creative ways to make this tragic scenario come to pass. For instance, the Dursleys could have made a deal with some dark forces, trading Harry's life for their own 'normal' life, and those dark forces would use powerful and insidious magic to end Harry's life.
It might be that in that particular fanfiction, the author was exploring different themes such as sacrifice on a grander scale. Harry Potter sacrificing himself to save the entire wizarding world in a more permanent way than in the original story. For example, perhaps the threat in the fanfiction was so great that his death was seen as the only solution to end the chaos and darkness.
The wizarding world would lose its 'Chosen One'. Voldemort would probably remain in power. Without Harry to oppose him, there would be no one to fulfill the prophecy. The wizarding world would likely be plunged into deeper darkness and tyranny under Voldemort's rule.
Perhaps in this fanfiction, Harry didn't have the right items or knowledge at the crucial moment. The Elder Wand might not have recognized him as its true master, or he could have been betrayed by someone he trusted, which led to his death. Also, the magical world could have been in a more chaotic state, with darker magic being more prevalent and overwhelming Harry's defenses.
In this fanfiction, perhaps Dudley's envy of Harry's magical world finally boiled over into uncontrollable rage. He might have found a way to cross into the wizarding world without anyone knowing. And in a moment of extreme jealousy and anger, Dudley could have used some kind of weapon or spell (maybe through some dark magic loophole) against Harry, which unfortunately led to Harry's death. Fanfiction allows for these extreme and unexpected plot twists.
One possible storyline could be that the Dursleys' pet, perhaps their cat, discovers Harry's wizarding abilities before the Dursleys do. It might then have some comical or tense interactions with Harry, like trying to stop him from using magic in the house for fear of getting in trouble itself.
One possible plot could be that the Dursleys receive a threat from the wizarding world that they can only be protected from if Harry stays with them and helps. Harry, being a good - hearted person, decides to do so and in the process, he starts to understand them better and grows to love them.
One possible motive could be extreme revenge. After years of being mistreated, locked in a cupboard, and generally being made to feel unwanted, Harry might snap in fanfiction. Another could be a sense of self - preservation if the Dursleys were somehow involved in a plot against Harry's life in the fan - created plot.
In some versions, Harry might be saved by his magical abilities emerging in a crucial moment. Maybe he uses magic to make food appear for himself, defying the Dursleys' cruel intentions.
It can make readers view the original series as more fragile. Since Harry Potter is the main hero in the original, his death in fanfiction shows that the world J.K. Rowling created can be drastically altered.
One possible scenario could be that a group of Hogwarts students, while exploring a hidden cave near the Forbidden Forest, accidentally trigger a magical trap. Maybe they were searching for some rare magical ingredient for a potion. The trap could be a spell that causes the cave to start collapsing, like the rocks begin to fall and the entrance gets blocked. They then have to use their magic skills, like levitating the rocks or using the reducto spell to clear a path out.