This episode opens on the subway with a riot. People start fighting and a cop is shot dead but there is no explanation for this mass hysteria. The alpha team is brought in and Rachel picks up weird from a teddy bear. After watching the surveillance video, they focus in on a young woman as responsible for the violence. Lee believes that she is releasing pheromones which cause people to lose control and become violent.
They manage to track her to a halfway house but she gets away and instead they capture Matthew Hurley. When they take him back to the office, he tells them that they are looking for his sister and that he is immune to the effects of her pheromone throwing. Lee believes that his immunity is based in his constant exposure. Gary discovers that she has brought a ticket for a bus but when he goes to tell Lee, Don Wilson is talking to Lee. Don is not patient and wants the girl contained and brought to Binghamton immediately. Bill then escalates the situation by announcing that the girl they are looking for is not Hurley's sister. Lee realizes that they alpha is actually Matthew but before he can warn anyone, Matthew releases another round of pheromones causing everyone to lose control. A fight breaks out, Rachel who was on the phone at the time ends up screaming at her mother for the first time. The fight continues to escalate with punches being thrown and Bill is the only one who manages to stay in control. Don ends up being shot dead by another federal agent.
When they get to the bus terminal, Matthew is already there. He tells Tracy that everything he did was for her. I have to say that I was so happy to see Tracy reject this and tell him that he had to stop. It would have been so easy for her to buy into the myth that her love had the potential to change and save Matthew. Matthew refuses to turn himself in and releases yet another round of pheromones. A small riot ensues and he hides on a bus until Bill boards and knocks him unconscious before he can escape.