One great fanfiction could be about Scott exploring the full extent of his True Alpha power. He might use it to protect his pack from a new and powerful threat. For example, a group of supernatural hunters who don't follow the normal rules. Scott's power as a True Alpha could give him the ability to sense their plans before they act.
Perhaps in fanfiction, Scott's True Alpha power gives him the ability to heal not just physical wounds but also emotional and spiritual ones. He could use this power to help his pack members who are suffering from past traumas. This would make him not just a powerful leader but also a healer within the pack, further emphasizing his True Alpha status.
Well, perhaps the alpha pack kidnaps Scott to use him as a bargaining chip against his friends. They might want something in return like some kind of powerful artifact or information.
Scott is surely a main character. And then, depending on the fanfic, there could be Scott's friends who would become main characters as they try to rescue him. They might include characters like Stiles or Allison. And of course, the alpha pack members are central to the story as they are the kidnappers.
Well, perhaps the story could start with Stiles facing some great danger that forces him to undergo a transformation into an alpha. He might have to battle some powerful enemies and in the process, learn to control his new alpha powers. It could also involve his relationships with other characters changing as he takes on this new role.
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.
Partly. The movie takes inspiration from actual incidents, but it's not a 100% accurate account. Some elements might have been fictionalized to make it more engaging for the audience.