It could be that Naruto has an epiphany about love and friendship. He might realize that his love for Sakura was more of an infatuation based on their childhood experiences. As he matures, he understands that true love should be mutual and free. So, he decides to let go of Sakura to find a relationship where his feelings are reciprocated, and also to respect Sakura's own choices.
Another possibility is jealousy. Maybe in the fanfic, Sakura shows more interest in another character, like Sasuke perhaps, and Naruto, who has his own feelings for Sakura, snaps out of envy. It's a common trope in fan - made stories to play with the characters' emotions like this.
One reason could be that she realizes she has been too dismissive of Naruto's feelings for her. She might have led him on or been cruel in rejecting his advances in the past. Another reason is that she finally understands how much Naruto has sacrificed for the village and for her personally, and she feels guilty for not showing him more respect and gratitude earlier.
It could also be a part of some sort of training gone wrong. In the world of Naruto, they often engage in intense training. If Sakura and Naruto were sparring and Sakura pushed Naruto too far, perhaps by taunting him about his strength or his progress compared to Sasuke, Naruto might lose his temper and punch her.
Perhaps it's a training exercise that gets out of hand. In the world of Naruto, intense training often mimics real battles. If they were sparring and emotions ran high, it could turn into a full - fledged fight. Also, Sakura might be trying to prove herself to Naruto, and Naruto, not understanding her intentions, might respond aggressively.
In some fanfics, Naruto may ignore Sakura because he has his own emotional traumas to deal with. He might find Sakura's presence a reminder of things he wants to forget or move past, so he chooses to keep his distance. For example, if he has faced a lot of rejection from her in the past, he could decide to just cut her out of his life.
It could also be that Naruto is forced to leave Sakura due to some external threat or danger. For instance, if there is an enemy targeting Naruto and he fears that being around Sakura will put her in harm's way, he would choose to leave to keep her safe. This is in line with Naruto's selfless nature as seen throughout the series.
In a fanfic, it could be for comedic purposes as well. The idea of Sasuke trying to act like Sakura while tricking Naruto can lead to some really funny situations. Maybe Sasuke is forced into this by some strange situation or magic. And he has to keep up the act of being Sakura, which includes mimicking her mannerisms and speech patterns, all while trying to fool Naruto. This could create a lot of humorous misunderstandings and interactions within the story.
In this kind of fanfic, one possible reason could be unrequited love. Naruto might have felt so hopeless about his feelings for Sakura never being returned that he saw no way out. He had always been in love with her, and if she continuously rejected him and perhaps even chose someone else, it could have broken his spirit to the point of self - destruction.
One reason could be that Naruto has grown weary of Sakura's unrequited love for Sasuke. He might feel like she's always focused on Sasuke and doesn't truly see him, Naruto. Another aspect could be that Sakura's constant nagging or her over - emotional outbursts have started to grate on Naruto over time. Maybe he's also tired of having to be the one to always cheer her up when Sasuke - related things go wrong.
One possible reason could be that Naruto has his own goals and missions that he is so focused on that he tries to avoid distractions, and Sakura might be seen as a distraction in some sense. For example, he is always aiming to become Hokage and improve his ninja skills, and any personal relationship drama could get in the way of that.