Perhaps in the fanfiction, Naruto disappears after the war because he has a secret mission. The war has unearthed some dark secrets about the ninja world that he has to deal with alone. It could also be that he has been affected by some sort of post - traumatic stress. The horrors of the war are too much for him to bear, and he leaves to try and heal in solitude. Or he may have made a deal with some powerful entity during the war to ensure the safety of the village, and part of that deal is his disappearance.
In fanfiction, Naruto might disappear after the war due to the realization that his presence is causing more harm than good. His power and fame could be attracting unwanted attention to the village. He could also be on a journey to find a way to truly end all conflicts in the ninja world. There are also chances that he is influenced by an external force, like a mysterious ninja from a far - off land who convinces him that leaving is the best option for the future of the ninja world.
One reason could be that he feels burdened by the expectations and the weight of his newfound peacekeeping role. He might want to escape the constant pressure and find himself. Another possibility is that he discovers a new threat during the post - war reconstruction and decides to go into hiding to investigate it without causing panic. Maybe he also has some personal issues related to his relationships, like feeling estranged from his friends who have changed after the war, and he needs time alone to sort things out.
One possible reason could be that he is suffering from post - traumatic stress disorder. After all he has been through, he might want to isolate himself from the wizarding world to heal. Another reason could be that he feels a sense of guilt for those who died in the war, and disappearing is his way of punishing himself.
One possible reason could be political. After the war, the villages might be restructuring and Naruto, with his great power, could be seen as a threat. Another reason might be related to the secrets he knows. Maybe some powerful figures don't want him to expose certain things. Also, his Jinchuuriki status could play a role. People might still be fearful of the power within him even after the war.
Well, one reason could be that he's kidnapped by a secret organization. They might see his potential and want to use him for their own evil plans.
Another reason could be political. After the war, the power dynamics in the village might have changed. There could be new leaders or groups who saw Naruto as a threat to their authority. They might have plotted to make him look bad and turn the villagers against him, causing him to feel betrayed by the very people he fought for.
At first, the village would be thrown into chaos. People would be speculating all kinds of reasons for his disappearance. His closest friends would be heartbroken and determined to find him. The elders of the village would be concerned about the political implications. Without Naruto, their main source of power and protection seems to be gone. However, some might also see it as an opportunity for a new era in the village, one that is not so reliant on a single individual, but this view would be in the minority at the start.
One reason could be that he's being hidden by some powerful magic from a group that wants to use him for dark purposes. Maybe there are dark wizards who know of his future importance and want to either kill or control him, so a good wizard has made him disappear.
Well, one reason could be that he's on a secret mission for S.H.I.E.L.D. that requires him to go undercover and cut off all contact. Maybe he's investigating a new super - villain threat that's too dangerous to let anyone know about.
One reason could be that he feels a sense of disillusionment. After the war, he might see that the village he fought so hard for still has deep - seated problems and prejudices. He might think that leaving is the only way to find true peace for himself. Another reason could be to protect the village from any potential threats that might target him. If he's away, those threats might not come to Konoha.
Maybe it was a wolf. Wolves are known to prey on sheep. In many old stories, wolves are the main cause of sheep disappearing from the farms.
One possible reason could be that Sasuke might have gone too far in his pursuit of power even after the war. He could have been a threat to the newfound peace in the ninja world, and Naruto, as the protector of peace, might have felt he had no other choice.