One possible reason could be that Naruto has a dangerous mission that only he can undertake. The safety of the village or the greater good might demand his immediate departure, even though it's hard for him to leave Hinata in such a state.
Maybe Naruto is forced to leave due to some political reasons within the ninja world. There could be some powerful forces that require him to be away from Konoha and his family for a while. Another reason could be that he has to go and find a cure or an important item for Hinata's or the baby's health, if there are some potential threats.
One reason could be envy. Maybe Naruto sees Hinata as having something he doesn't, like a more stable family situation, and he lashes out in jealousy. Another reason might be that he's just being a typical, rambunctious kid who doesn't realize the impact of his words or actions on Hinata.
One possible reason could be that she realizes she truly loves Naruto too much to be apart from him. Maybe she left because of some misunderstanding or external pressure, but then comes to understand that her place is by his side. Another reason might be that she sees how much Naruto has grown and changed, and regrets not being there to support him during that journey. Also, she could have found that life without Naruto is just not as fulfilling as she thought it would be.
A simple reason could be that they are poisoned. An enemy might have laced their food or drink with a slow - acting poison that causes them to faint at an unexpected moment.
In certain fanfictions, Naruto might have a pre - existing relationship or unrequited love for someone else. This could make him overlook Hinata or even seem to dislike her because his heart is set on another character.
One possible reason could be a misunderstanding. Maybe Naruto was in a situation where it looked like he was cheating, but in reality, it was all a big mix - up. Another reason could be that the writer of the fanfiction wants to explore a darker side of Naruto's character. Or perhaps there's some sort of outside influence, like an enemy using some kind of mind - control on Naruto to make him act out of character.
In some fanfictions, external forces might be the cause. Perhaps a powerful enemy threatens Hinata and tells her that staying with Naruto will put him in danger. So, to protect Naruto, she decides to abandon him. This adds a tragic and self - sacrificing element to the story.
They might leave to seek new forms of power or knowledge. There could be things outside of Konoha that they believe will help them become better at their ninja skills. For instance, they might have heard of a special dojo or a hidden scroll in another land that could enhance their abilities.
One possible reason could be a huge misunderstanding. Maybe he thought Hinata did something really bad to his friends, like unknowingly leading the enemy to them. Without knowing the truth, his hot - headed nature made him lash out.
One reason could be to seek new challenges. In some fanfictions, Naruto might feel that he has accomplished all he can in the Elemental Nations. He has protected his home, become Hokage, and now he wants to explore the wider ninja world or even other realms that are unknown to the Elemental Nations.
One reason could be to protect Konoha from a great danger that he can only face by leaving. Maybe there's a powerful enemy who has a vendetta against Naruto but would spare Konoha if he goes far away. Another reason might be a sense of self - exile due to some event that made him feel he no longer belongs in Konoha, like a misunderstanding where the villagers turn against him again.