Two months after the end of Season 3 and still healing from tragic losses (Allison and Aiden), Scott (Tyler Posey), Stiles (Dylan O'Brien), Lydia (Holland Roden) and Kira (Arden Cho) return to a new semester of school with more human worries than supernatural, while also trying to help their new friend, Malia (Shelley Hennig), integrate back into society. But Kate Argent's (Jill Wagner) surprising resurrection brings a new threat to Beacon Hills along with the emergence of another mysterious enemy known simply as The Benefactor. Scott must also uphold the responsibility of his first Beta werewolf, Liam Dunbar (Dylan Sprayberry).
The team has their hands full with Liam and Malia when the full moon arrives. The 'Axe Murderer' harms Peter and reveals that Derek is next on his 'list'. Lydia cracks the code and finds a list of all supernatural creatures in the town.
As another name is scratched off the list, Lydia is required to find the second key, thus revealing more targets. Scott, Stiles and Kira are on high alert after realizing that the assassin is on the lacrosse team.
A frantic call to the CDC has everyone paranoid, especially since it was designed to target werewolves. Scott, Malia and Kira lock themselves in the Hale vault, unaware of their salvation within their grasp.
With Noshiko's help, the team come up with a plan hoping to reveal the benefactor's identity. But Kate's arrival threatens to ruin it all. Malia comes face-to-face with Peter in the Hale vault, thus delving into her past.
After a vain attempt to kill Parrish, it's clear that almost everyone has access to the dead-pool. Lydia dives into her grandmother's past, uncovering yet another list which leads her to Eichen House. The team soon realizes no one is safe.
Meredith is brought in for questioning, but refuses to talk to anyone but Peter. Stiles and Malia head over to the lake house wherein lies the dead-pool. Scott, Derek, Kira and some others take a stand against the assassins out for blood.
Deaton visits Eichen House in a search for answers to Derek's situation; Liam's horrific hallucinations costs a win for the lacrosse team; Scott plans a magical night for Kira and himself which soon turns into a nightmare beyond imagination.