After relocating to a new office in Queens, New York, the Alpha team is settling in-or trying to. Nina is upset because the office is so far away form everything, Rachel is disgusted by how dirty the office is, Gary is distracted by a buzz that no one else can hear, Hicks isn't sure he belongs, and Bill, well, he's just grumpy.
Upstate, a deadly traffic accident near Binghamton, NY leaves several people dead and a new Alpha out on the streets. Marcus Ayers, Dr. Rosen's very first Alpha patient, has escaped from Binghamton Special Research Facility (the place where Alphas who misuse their abilities get rehabilitated) and he seems to have a violent agenda. Rosen knows all too well that Marcus is capable of controlling almost everything around him, which makes him extremely dangerous and almost impossible to catch.
Whatever Marcus' agenda, Dr. Rosen is clearly a part of it. Marcus left clues near the scene of the crime that lead Rosen to a series of memories about how he first met Marcus and how both his powers and his acute paranoia developed over time.
Back at the office the next day, Ms. Sullivan has shown up and she seems to know about each member of the Alpha team. The reason, it turns out, is because Agent Sullivan is temporarily replacing Agent Wilson while he's on another assignment. Sullivan tells Dr. Rosen that she thinks Marcus blames him for his incarceration and plans to kill him. After the full team briefing Nina is angry with Dr. Rosen for keeping Marcus' escape a secret since she knew him well.
Rosen asks Hicks to study Marcus since they have similar powers and Rachel finds ash residue on the quarter Marcus left behind, which leads Dr. Rosen to Marcus' old apartment building, where he burned his previous roommates. Sure enough, Marcus is waiting for Dr. Rosen there-but he's not the only one. Binghamton's Department of Defense liaison Nathan Clay has been using the unwitting Dr. Rosen to track down Marcus.
After Marcus uses his powers to escape, Rosen investigates his claims that something awful was happening at Binghamton by asking Dr. Singh. He is surprised to find out that Singh was planning to lobotomize Marcus. Only moments after confessing this fact to Dr. Rosen, Marcus kills Dr. Singh.
By tracing the flower pollen from a chess piece that Marcus left at the scene of Dr. Singh's murder, Gary is able to locate Marcus but, of course, since he is a master strategist, Marcus is already waiting for them. The team thinks that Marcus is after Nathan Clay, but when everyone is distracted Marcus kidnaps Dr. Rosen so that he can explain that a war is brewing between Alpha humans and non-alphas.
Even though he surrenders, Clay shoots Marcus in the chest. When they can't find his body, however, the team begins to suspect that Marcus may have faked his death to prepare for the coming war.