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Scott and Stiles start the episode hiding from the alpha wolf in their high school. They spend most of the episode running and hiding from the scary beast. Scott texts Allison to come to the school, only it wasn't Scott.
Allison shows up to the school with Jackson and Lydia, and they join the other two boys in running from the alpha wolf. Once the alpha finds Scott, he doesn't hurt him. Later on the alpha forces Scott to turn wolf, and also controls Jackson in some way.
Scott realized that the alpha wants him to join his pack. In order to do that, Scott needs to get rid of his old pack, which means killing Allison, Jackson, Lydia and Stiles. When the alpha controls Scott, he wants to kill his friends.