Well, it could be one of the rivals of the empress or someone with a hidden agenda. Maybe it's related to power struggles or personal vendettas. But it really depends on the specific plot and characters of the manga.
Papyrus can also be a victim of kidnapping in fanfictions. His naive and friendly nature makes him an easy target in some stories. His kidnapping could lead to Sans going on a desperate search for him, which would involve a lot of action and emotional moments as Sans tries to rescue his brother.
The Naraku would be a likely kidnapper. He is always plotting against Inuyasha and trying to get his hands on the Tessaiga. Kidnapping Inuyasha would be a way for him to either steal the sword or find a way to break Inuyasha's spirit so that he can no longer oppose him.
It could be a new character created specifically for the fanfiction. Maybe a young scientist who is working on a project related to the super - soldier serum. Since Bucky has a history with the serum, this would create an interesting dynamic.