One way could be by exploring misinformation. Maybe Naruto was told lies about his parents' actions that made him believe they were bad. For example, if he was misled to think his father was responsible for some great tragedy in the village.
One way could be that his parents were forced into it. Maybe they were under some powerful dark magic or mind - control that made them seem to betray Naruto. For example, an evil villain could have manipulated them to make Naruto think they don't care about him.
Perhaps his parents were misled to believe that Naruto was a threat to the village. They might have been fed false information about Naruto being a potential danger, like being a vessel for a great evil. So, in an attempt to protect the village they loved, they made the tragic decision to kill him.
One reason could be misinformation. If in a fanfiction, Naruto is fed false information about his parents' actions, he might come to hate them. For example, if he's told that his parents were responsible for a great tragedy that he believes in without knowing the truth. Another factor could be the feeling of abandonment. Since Naruto grew up alone, if a fanfic writer emphasizes this aspect and makes Naruto believe his parents willingly left him, he could hate them.
A plot for this type of fanfic could revolve around Naruto's inner turmoil. He could be constantly haunted by the question of why his parents neglected him. This could lead him to make some bad decisions, like getting involved with the wrong people. However, through a series of events, he starts to realize that he can create his own family and support system. He then begins to build a new life for himself, one that is not defined by his parents' neglect but by his own strength and the relationships he chooses to cultivate.
Perhaps his parents were part of a secret and evil organization all along. They pretended to be good but in fact were planning something big and Harry was just a pawn in their plan. So they betrayed him by leaving him exposed to danger or even trying to harm him directly. In the fanfiction, Harry could then go on a journey to discover the truth about his parents and their real motives.
Well, one way could be that the villagers' long - hidden fear and jealousy of Naruto's power finally boil over. Maybe they believe some false rumors that Naruto is about to destroy the village. So, in a fit of panic, they turn on him all at once and overpower him.
In this fanfiction scenario, it could be that an enemy uses some sort of mind - control jutsu on Naruto's family. The family, under the control of this jutsu, doesn't recognize Naruto as their own and kills him. This would add an element of tragedy as Naruto would be killed by those he loves and trusts the most without them being fully in control of their actions. It would also open up the story for a revenge plot by Naruto's friends or other allies against the enemy who controlled his family.
One way it could be developed is that his sister might be jealous of Naruto's growing popularity or skills. Maybe she feels overshadowed and starts to bully him by spreading false rumors about him in the village. This could lead to Naruto feeling more isolated and misunderstood, even as he tries to prove himself.
One possible reason could be that Naruto has some sort of power within him that they fear. Maybe it's a power that they don't understand and think could be dangerous, so they hate him out of fear.
In some fanfictions, Naruto might find a super - powerful jutsu or artifact. For example, he could discover a long - lost forbidden jutsu that has the power to bring the dead back to life. Or perhaps he stumbles upon a magical item during one of his adventures that is said to be able to revive the deceased.