Often, it's the hunters who turn out to be the antagonists. Hunters who don't believe in the good of the supernatural beings associated with Stiles. They might think that by kidnapping Stiles, they can get information about the other supernaturals and eliminate them. Also, some fanfictions feature a deranged human scientist who wants to study Stiles because he seems to be a key to understanding the supernatural world, but they go about it in a very unethical way by kidnapping him.
In many Dramione kidnapped fanfictions, Death Eaters or their remnants are common antagonists. They might want to use Hermione as a bargaining chip against the Order of the Phoenix or to gain some dark magic knowledge from her.
It could be a rogue werewolf. Maybe this werewolf has a grudge against Stiles' pack and thinks that by kidnapping Stiles, he can get some sort of revenge or leverage.
Survival is a major theme. Stiles has to find ways to endure the torture and escape his captors. Another theme is the psychological impact. The trauma he experiences changes his perspective and relationships.
The Akatsuki could also be antagonists in an Iruka kidnapped fanfiction. They might believe that Iruka has some information about the jinchuriki, especially since he is close to Naruto. Or there could be a new, made - up antagonist in the fanfiction, like a powerful dark wizard who has set his sights on Iruka for some unknown but sinister reason. This new antagonist could add a fresh and unique element to the story.
There could be a group of hunters who see Stiles as a new threat now that he is an alpha. They might think he will be more dangerous and unpredictable, so they target him. Also, some supernatural creatures that have a vendetta against alphas in general could oppose Stiles.
His friends, of course. Scott would be one of the most likely rescuers. As Stiles' best friend and a werewolf, he has the strength and loyalty to track Stiles down. Lydia might also be involved. With her banshee powers, she could sense Stiles' distress and lead the others to him. Another possible rescuer could be Derek. He has a lot of experience dealing with dangerous situations and might feel a sense of obligation to save Stiles, especially if he realizes Gerard is involved.
Well, sometimes in these types of fanfictions, a plot twist can be that Stiles finds out Gerard is related to him in some unexpected way. This could completely change the dynamic of their relationship. Maybe Gerard is his long - lost relative, and this revelation makes Gerard have second thoughts about his actions. Or, there could be a plot twist where the place where Stiles is kidnapped has some sort of magical property that either aids or hinders his escape. For instance, it could be a place that nullifies certain supernatural powers, making it more difficult for Stiles to use his usual means of getting out of trouble.
Typical antagonists in this kind of fanfiction can be various. The Sith, as we know, are always a likely candidate. They seek power and might see a kidnapped Jedi as a means to an end, like getting access to ancient Jedi secrets. But it's not just them. There could be rogue elements within the galaxy who oppose the Jedi for different reasons. Some might be power - hungry warlords who think a kidnapped Jedi can give them an edge in their territorial disputes. Also, there are the shadowy criminal organizations that might kidnap a Jedi for ransom or to sell on the black market. They don't care about the Jedi - Sith conflict; they just see an opportunity for profit or power.
Some powerful and evil supernatural creatures could also be antagonists. For example, a powerful dark witch who wants to use Peter and Stiles for some dark ritual. She might try to manipulate them or put them in dangerous situations to achieve her goals.
Sometimes, the plot twist is that Stiles is actually in on the kidnapping in a way. Maybe he's trying to protect his friends from a greater danger by faking his own kidnapping. So all the while his friends are searching for him, he's actually on a secret mission of his own, which is revealed later in the story and makes for a really interesting read.