One idea could be that their own village betrays them. Maybe there's a power - hungry leader who sees Naruto and his sister as threats to their new regime. They could be framed for a crime they didn't commit and then forced to flee the village. In the process, they might have to rely on some unlikely allies they meet on their journey, like a group of outcasts who also have a grudge against the village.
Another scenario could be that they are betrayed by an organization that was initially pretending to help them. This organization might have been using them to get access to some secret jutsu or valuable information. Once they get what they want, they turn on Naruto and his sister. Naruto and his sister then have to figure out how to expose this organization and clear their names.
They could lose their home. If the betrayal is by the village, they would no longer be welcome there. They'd have to find a new place to live, which could be a difficult task as they are being hunted. They might end up in a hidden, desolate place where they have to start from scratch, building shelter and finding food.
In a more complex scenario, Naruto could be influenced by an outside force. Let's say an enemy of Konoha uses mind - control or some form of manipulation on Naruto. They make him believe that the ANBU is the enemy of the village and that he needs to take them down. As he betrays the ANBU, he slowly starts to realize that he's been used, but by then he's already in too deep and has to find a way to fix the situation and regain the trust of his friends and the village.
One idea could be that in the fanfiction, Hinata is under the influence of a powerful genjutsu. This genjutsu makes her see Naruto as a threat to the Hidden Leaf village. So, she betrays him to protect the village in her distorted view. It could lead to a lot of inner conflict for Hinata once she realizes the truth and Naruto having to deal with the pain of her betrayal.
One idea could be that the girlfriend, perhaps under the influence of an enemy, reveals Naruto's bloodline secrets to those who would use it against him. For example, she might be tricked into thinking she's helping Naruto in some way, but actually endangering him.
In 'naruto betrayed fanfiction', sometimes Naruto is betrayed by the hidden village itself. They might not support him when he needs it most, perhaps during a major battle against a powerful foe. The village could cut off his resources or even try to capture him. Also, a betrayal could come from a character who Naruto trusted to train him, but instead uses his training to turn Naruto into a weapon for their own evil purposes.
Naruto's power might also be affected. If he was betrayed, he could lose the will to fight or train. He might even start to doubt his own purpose. This could lead to a decline in his abilities, which in turn could put the village at risk if he was its main protector.
In the Naruto series, Naruto doesn't have a biological sister in the original story. So in this fanfiction, the author probably creates a new character to be his sister. It could be an original character with unique abilities and a complex backstory that leads to the situation where Naruto dies by her hand.
The sister could be under the control of a powerful god or goddess who has a grudge against Percy. She might be forced to betray him. For instance, she could lead Percy into a trap set by the god. She could lie to him about a mission, saying it's a rescue mission but in fact it's a trap where the god is waiting to take revenge on Percy for some past deeds. This would be a really heart - breaking betrayal for Percy as he trusts his sister.
His reaction would depend on how the betrayal was presented. If it was a sudden revelation, he would be shocked and devastated. He may start to question his own worth, thinking that if his own parents could betray him, what was wrong with him? He could also become more reckless in his actions, not caring about the consequences as much since he felt like he had already lost the most important thing. This new Naruto could also be more empathetic towards the villains in the story, understanding their feelings of being wronged or betrayed in some way.
In this fanfic scenario, Naruto's character could take a darker turn. Maybe he becomes more solitary and distrustful. His sister, on the other hand, might be favored by Kushina but have her own internal struggles. The story could explore how Naruto overcomes his feelings of being abandoned and reconciles with his family.