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.
Well, often in these fanfictions, Stiles becomes more confident. His physical appearance might also change, like he could start dressing better or have a new haircut that gives him a 'hot' look. For example, he might start wearing more stylish clothes that show off his personality.
Stiles usually reacts with a mix of fear and defiance. He's afraid because he's in a dangerous situation, but his strong - willed nature makes him defiant. For example, in many fanfictions, he'll shout at Peter, trying to show that he won't be easily broken.
He could use his intelligence to manipulate Kate. Maybe he convinces her that he is more useful to her if he is free, and she lets her guard down long enough for him to make a run for it. Also, he could have some hidden skills or knowledge that he uses to break free. Say he knows a spell or a code that unlocks his restraints or the door to his prison.
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.
There's a fanfiction where Stiles is kidnapped by a supernatural being and tortured in a hidden lair. It focuses on his attempts to escape and the friendships that help him through it. The author does an excellent job of building tension throughout the story.
It could be his love interest, like I mentioned before, Lydia. She might reject him because she's too focused on her own goals or perhaps she doesn't see Stiles in that way at the time. Their relationship has always been a bit complex in the show, so this would be a likely scenario in fanfiction.
One great fanfiction could be 'The Abduction of Stiles'. In this story, Stiles is kidnapped by a mysterious group. The author does a wonderful job of building suspense as his friends race against time to find him. It has some really intense moments and great character development.
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.
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.