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.
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.
In some fanfiction, the idea of Harry Potter being betrayed by his parents might be justified through a complex web of magic and prophecy. Maybe the parents thought sacrificing Harry was the only way to save the wizarding world from a greater evil. However, this goes against the essence of their characters in the original books.
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.
In such a fanfiction, perhaps the parents were forced to betray Harry due to some dark magic or a powerful enemy threatening them. Maybe they had to give up Harry to save the wizarding world from an even greater evil.
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.
One way could be through a dark magic spell that was secretly cast long ago. Maybe Voldemort had a plan to create a powerful heir, and he used some complex magic on Harry's mother. In this fanfiction, Harry might struggle with his new identity, feeling torn between the good he was raised with and the dark heritage from Voldemort. He could have inner battles over his natural inclination towards dark magic due to his bloodline, while also trying to resist it because of his friends and the values he learned at Hogwarts.
The author could start by showing small signs of the abuse, like Harry flinching when someone raises their hand near him, which implies he has been hit before. Then gradually reveal more details of the abuse through his memories or nightmares.
It could be that his parents were trying to protect Harry in a really messed - up way. They might have thought that by 'betraying' him, like sending him away or making him seem like an outcast, they could keep him safe from a much greater threat. Maybe they knew some prophecy about Harry and thought this was the only way to ensure his survival. They might have made a deal with some dark force, believing they could outwit it in the end but ended up being seen as traitors by Harry and others.
In a fanfiction where Naruto is betrayed by his parents, the implications are vast. Firstly, Naruto's motivation which was previously driven by a desire to gain recognition, including from his absent parents, would be turned on its head. He may no longer strive for the same things. His relationships with his mentors like Iruka and Kakashi could also be affected as he struggles with this newfound sense of abandonment. Moreover, the village's perception of him might change as he becomes more bitter. This could lead to a split in the village, with some supporting Naruto in his new, darker path and others trying to bring him back to his former self.
He would probably be very confused and heartbroken at first. He might isolate himself from others as he tries to make sense of what has happened.