One common theme is loyalty. They often show how Peter and Stiles are loyal to each other no matter what. Another is the theme of protection, as they protect each other from various threats.
Well, a common plotline is the discovery of their mate bond. In many fanfictions, Stiles might not be aware at first that he is Peter's mate. So there could be a lot of confusion and self - discovery on Stiles' part. Peter, on the other hand, would be trying to court Stiles in his own way, which could lead to some really comical situations. Also, there could be a plotline where their relationship is challenged by the pack. The pack might not be accepting of their bond initially, thinking that Peter is too dangerous for Stiles. But through their love and determination, they prove that their bond is strong and worth fighting for.
There's also 'Peter and Stiles: Unlikely Mates'. This fanfic focuses on how they overcome their differences and form a strong bond. It has some really engaging plot twists.
Stiles might become more confident. Usually, he is a bit of a nervous character, but with Peter as his mate, he has someone who believes in him wholeheartedly. Peter, in turn, could become more gentle. His usually harsh and calculating nature softens as he is in a relationship with Stiles. For example, he might be more patient when dealing with Stiles' sometimes erratic behavior.
There could be other members of Peter's pack such as Derek. Derek often plays an important role in stories related to packs. He might be initially skeptical of Stiles being part of the pack.
On the other hand, Stiles is also known for his quick thinking. He might start to try and bargain with Peter. He could offer to help Peter in some way if Peter lets him go. For example, if there's a problem in the supernatural community that Peter is facing, Stiles could say he'll use his human ingenuity to solve it. Also, Stiles could be angry. He might start shouting at Peter, calling him out on his actions, and trying to make Peter see how wrong this is.
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.
Overcoming obstacles is also a big theme. There could be things like pack politics, family issues, or other supernatural threats that they have to deal with as a couple. Their bond as mates gives them the strength to face these difficulties.
At first, it might be a tentative alliance. Stiles could be initially drawn to Peter for his knowledge. Peter, seeing Stiles' potential, starts to include him more in his plans. As time goes on, they might develop a mutual understanding. Stiles begins to trust Peter more and more, and Peter starts to value Stiles not just for his help but also as a friend or something more.
It could be that Stiles is in some kind of danger, perhaps from another supernatural being. And he goes to Peter because Peter has certain powers or knowledge that could protect him. For example, Peter might know how to defeat a particular enemy or how to get out of a tricky situation involving magic or some other supernatural element.