Often, the themes include adaptation. Stiles has to adapt to his new fox body, which might have different physical abilities and limitations. There's also the theme of mystery, like trying to find out how he got turned into a fox and how to reverse it. And of course, there's the theme of relationships. His relationships with his friends, family, and love interests will all be affected by this transformation.
One possible plot could be Stiles' struggle to adapt to his new female body. He might have to deal with different social expectations and how his friends react to his new appearance. Another plot could involve Stiles trying to find a way to turn back into his male self while facing various challenges along the way.
There might be a jealous friend or acquaintance who feels that Stiles, as a girl, is getting too much attention. This person could then start spreading rumors or causing trouble for Stiles in an attempt to bring her down.
Scott would probably be very protective. He'd feel responsible for taking care of Stiles and making sure he doesn't get into too much trouble. Lydia might be initially shocked but then use her intelligence to try and figure out how to reverse the situation. And Derek, well, he'd probably be a bit annoyed at first but would also end up being one of Stiles' protectors.
In some fanfictions, a possible plot could be that Stiles, as a kid, has a different perspective on the supernatural world around him. He might not be as afraid as he was when he was older. For example, he could befriend a supernatural creature that the older Stiles would have been more cautious about. This new friendship could lead to new alliances for the pack. Also, his family's reaction to his sudden transformation could be explored. His dad might be really confused and worried, while his friends are trying to keep it a secret from the wrong people in town.
Well, there are several out there. In some of these fanfictions, Stiles' transformation into a fox often leads to him discovering new abilities. For example, in a particular story, he finds out he can communicate with other forest animals in his fox form. This adds a whole new layer to the story as he uses this ability to help his friends. The change also affects his relationships, especially with his best friend. There's a lot of character development that can come from such a transformation in fanfiction.
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.
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.
His relationship with his friends would likely become more strained. They might be afraid of him or he might be afraid of hurting them. For example, his best friend Scott, who is also involved in the supernatural world, might be worried about Stiles losing his humanity.
The fanfiction could be about the adventures Stiles and the puppy have. They could go on hikes together in the forest near his town. During these hikes, they might encounter strange things or other supernatural beings. The puppy could either be scared or curiously investigate. Stiles would have to protect the puppy and also figure out how to deal with whatever they come across.