At the end of 3A; Allison, Stiles and Scott had agreed to be surrogate sacrifices to the nemeton, which would forever leave a scar, darkness, in their hearts. They would feel it everyday for the rest of their lives. Scott, Stiles, and Allison had entered into icy water, anchored by Deaton, Lydia, and Isaac respectively. They had found the nemeton, which was where Derek had sacrificed Paige, and Peter had sacrificed Jennifer.
The surrogate sacrifices would also turn the Beacon Hills back into a beacon for supernatural creatures, which would draw different creatures to the town from everywhere.
Scott had become an alpha, the alpha pack was destroyed, Deucalion could see again, and twins were turned into betas/omegas.
TEEN WOLF - SEASON 3, PART B
Synopsis: After the Nemeton was given life again by Scott and his friends, life in Beacon Hills would not be the same anymore. While Scott, Stiles, and Allison have to deal with their darkness within, new creatures are starting to inhabit the town. While some only want a place to live in, some do not have the same peaceful intentions. Meanwhile, Peter has different plans for the new residents and the True Alpha, Scott McCall.