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.
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.
Well, in some extreme fanfictions, it might be due to some kind of mind - control or dark magic that forces Naruto to do such a heinous act. But this goes completely against his character in the original series.
It could be that the family discovers a false prophecy about Naruto bringing doom. In the fanfiction, they might be so desperate to prevent this 'doom' that they decide to kill Naruto, not realizing it was a false prophecy all along. This would add a tragic element as their fear led them to commit an unthinkable act.
Well, one way could be that Padme is from a different ninja village and is on a secret mission. She gets close to Naruto to gain information about Konoha. When she gets what she needs, she betrays him by revealing his secrets or setting him up in a dangerous situation. For example, she could tell his enemies his fighting patterns or the location of his important allies.
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.
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.
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.
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.
In a fanfiction where Naruto is the villain, perhaps he becomes corrupted by the Nine - Tails' power. The constant struggle to control the fox within him finally takes a toll, and instead of fighting it, he gives in. He then uses the Nine - Tails' brute strength to wreak havoc. He might see the shinobi world as a place full of hypocrisy and decides to 'cleanse' it by force, attacking villages one by one, starting with Konoha, which he now views as a place of false promises.
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.