One possible reason could be the burden of his past. Naruto has faced a lot of hardships and the memories might be overwhelming him, making him want to be alone. For example, the loss of his master Jiraiya might have left a deep scar, and he might feel that isolating himself is the only way to deal with that pain.
One possible reason could be a misunderstanding. Maybe Naruto overheard something his family said that he misinterpreted as them not loving or believing in him. For example, if he heard them talking about his wild nature or his past mistakes in a way that he took the wrong way.
Perhaps he's dealing with some sort of trauma. For example, after the many battles he's been through, like the fight against Voldemort, he may be suffering from post - traumatic stress disorder. To cope with this, he isolates himself from others as he doesn't want to burden them or he's just too caught up in his own dark thoughts.
His relationship with the village would also change. The villagers, who have come to rely on Naruto as a hero, would be confused and perhaps a bit scared. Some might feel betrayed that he has isolated himself. But there could also be those who understand his need for solitude and wait patiently for his return.
One reason could be that Naruto has always been more attracted to those who understand his outcast past better. Sakura doesn't really have that kind of connection with him as she comes from a more normal background. So there's a lack of that fundamental understanding between them which hinders any romantic feelings.
One reason could be the fear of losing his friends. Naruto has always been very protective of his comrades. In some fanfictions, he might face a situation where he is on the verge of losing them, like a powerful enemy threatening to kill them all. This would make him afraid as his friends are his most precious things.
One possible reason could be a miscommunication between them. Maybe Anko feels neglected and then strays. Another reason might be that the writer wants to create a more complex and angsty plot.
One reason could be to show his maturity. Smoking is sometimes associated with adulthood or a more worldly view. So, by having Naruto smoke, the author might be trying to show that he has grown up and is dealing with more complex issues.
One possible reason could be the loss of a dear friend. Naruto forms deep bonds with his comrades, and if something were to happen to them, like Sasuke leaving again, it would break his heart and make him cry.
Some writers might do it for shock value. They want to create a story that stands out and goes against the norm of the relationship that fans are used to. By creating this unexpected plot, they hope to attract readers who are interested in seeing a different side of the characters.
One reason could be that Naruto feels constantly ostracized in the village despite his efforts to be accepted. In some fanfictions, he might run away because he discovers a dark secret about the village elders that makes him lose faith in the place he once called home.