It could be Orochimaru. He's always been interested in Naruto's power, especially the Nine - Tails within him. He might have come up with a new devious plan to capture Naruto and use his power for his own dark experiments.
Perhaps in this 'Boruto goes missing fanfic', Boruto is lured away by a mysterious figure who claims to have information about his future or his father Naruto's past. He follows this figure without thinking, only to find himself in a strange and dangerous place. His disappearance then sets off a chain of events in the village. People start to suspect that there might be a traitor among them who helped Boruto disappear. His teammates, like Sarada and Mitsuki, would then start their own investigation to find him, facing not only external threats but also internal doubts and suspicions within the village.
One possibility could be that he has gone into hiding to protect a secret. Maybe he discovered some dark magic plot and has to keep himself away from the wrong people until he can figure out how to stop it.
In this fanfiction, it might be that Percy goes missing because he is on a self - imposed mission. He could be trying to protect his friends from a danger he discovers, and he doesn't want to involve them, so he disappears without a trace. He might be in a far - off land, facing challenges all alone.
Another plot could be that Naruto goes missing because he's on a self - imposed exile. He might feel that he's putting his friends and the village in danger due to some new power he discovers within himself that he can't control. So, he decides to disappear to protect everyone.
One possible plot could be that Sakura has been kidnapped by a mysterious villain who has some vendetta against her or her friends. Another could be that she gets lost in a strange and magical realm while on a mission and her friends have to search for her. Maybe she has amnesia and wanders off, and everyone is trying to figure out where she is and how to bring her back to normal.
It could be a jealous rival. Maybe there's someone who is envious of Sakura's popularity or her skills, and decides to make her disappear. Another suspect could be a new character introduced in the fanfiction who has a hidden agenda.
If Snape goes missing, Hogwarts would be in chaos. His students would be worried and confused. The other teachers would have to take over his classes, but no one could replace his unique teaching style.