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.
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.
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.
It could be a new dark wizard that we haven't seen in the original series. This wizard might be jealous of Harry's fame and power and wants to eliminate him by making him disappear.
One possible plot could be that Harry has been kidnapped by a dark wizard who wants to use his powers for evil. Another could be that he has run away to find a way to defeat Voldemort on his own without endangering his friends. Maybe he's lost in a mysterious magical realm while on a quest and can't find his way back.
A new character introduced in the fanfiction might be the main suspect. This character could have some ulterior motives that are not clear at first. They might seem friendly but are actually behind Percy's disappearance. For example, they could be working for an evil organization that wants to use Percy for some dark purpose. So they plan his disappearance carefully to achieve their goals.
Well, it might lead to a series of investigations and discoveries. There could be hidden secrets about the mom's life that come to light. Or, it could trigger emotional turmoil within the family as they cope with the uncertainty.