One reason could be that Naruto realizes his feelings for someone else and doesn't want to mislead Sakura. In some fanfictions, Naruto might discover that his true love is Hinata and so he steps away from Sakura to pursue a relationship with Hinata without causing any confusion for Sakura.
In some fanfiction concepts, Naruto might have a prophecy or a special task that only he can fulfill. This task could demand solitude and a focus that doesn't allow him to be around Sakura. He may also have seen that Sakura has her own path to follow, like becoming a great medic - ninja, and he believes that she'll be better off without his interference, so he decides to leave her alone.
One possible reason could be Sasuke's pursuit of power. In many fanfictions, his thirst for greater strength might lead him to leave Sakura behind as he embarks on a solo journey to train in more dangerous and secluded places. He may feel that his goals are too dangerous for her to be involved with.
Maybe in this fanfiction, Sakura is involved in some kind of dangerous situation or plot that Naruto wants to avoid. He might leave to protect himself from getting too entangled. For example, if Sakura is part of a group that has different ideals which Naruto doesn't agree with and being around her means getting involved in those conflicts, he could choose to leave.
Maybe Naruto realizes that his feelings for Sakura are not as strong as he once thought. In the fanfiction, he could have met someone else or had an epiphany about his own emotions. He might leave Sakura to find his true self and explore different relationships.
One possibility is that Naruto realizes Sakura has feelings for Sasuke that he can't change, so he decides to focus on his own ninja journey alone and leaves her to figure out her relationship with Sasuke. He might feel that his presence is only causing confusion or getting in the way of her true feelings.
One possible reason could be his strong bond with Naruto. Their relationship has been through so much, and Sasuke might realize that Naruto understands him on a deeper level than Sakura. Maybe he feels that his journey and growth are more intertwined with Naruto's, and he values that connection more in this fanfiction.
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 some fanfictions, Naruto might leave the Anbu due to internal conflicts within the organization. There could be corruption or power struggles. Naruto, being the idealistic character he is, would not want to be part of such a messed - up system. He might have discovered some dark secrets about the Anbu that made him decide it was not the place for him.
One possible reason could be that she might have underestimated Naruto in the past. She often belittled his abilities and dreams, but as she grew and realized his true strength and determination, she felt the need to apologize for her previous behavior.
Another reason could be that Naruto is lured away by an external force. Some powerful figure or group might convince him that leaving his parents is for the greater good, perhaps in the name of protecting them or the village in a more effective way.
One possible reason could be to protect his family. In many fanfictions, Naruto might leave to draw danger away from his loved ones. He's always been self - sacrificing, so this would be in - character.