The crime-fighting team investigate the assassination of a police suspect. In the process they unearth a powerful cabal of criminals with superhuman capabilities.

Marcus, a former patient of Dr. Rosen's (David Strathairn) with the ability to set off a chain reaction of events with a predetermined outcome, escapes from Binghamton, a facility designed to detain and train Alphas. His escape causes Rosen to reexamine his tenuous relationship with the government, while he's being forced to get acquainted with his new Department of Defense liaison, Agent Sullivan (guest star Valerie Cruz). Meanwhile the rest of the team continues to balance their personal lives while continuing to work with Rosen.

The crime-fighting team investigate the assassination of a police suspect. In the process they unearth a powerful cabal of criminals with superhuman capabilities.

The team of Alphas, including new member Hicks (Warren Christie), relocates to new offices in Queens after the attack on Dr. Rosen's (David Strathairn) life. While adjusting to their new surroundings the team investigates a series of violent public riots that are breaking out on the east coast. The only connection between the riots is a runaway teen, an Alpha, who overproduces certain pheromones that causes people nearby to become violent. Rosen's team must find a way to stop this Alpha without losing control themselves.

Moving in on a Red Flag stranglehold, Dr. Rosen (David Strathairn) and his team encounter a group of Alphas with unfathomable abilities. After they escape capture, Gary (Ryan Cartwright) connects with their prisoner, Anna, an autistic young woman with the ability to understand all languages. Using her abilities Anna helps Gary, Rosen and the team uncover that Red Flag is plotting a large-scale terrorist attack that might change the existence of Alphas as we know it.

Rachel goes on a date that ends with a powerful kiss; Rosen's team officially joins the Defense Criminal Investigation Service, and their first case is to probe a series of deaths linked to a high school in Pennsylvania.