Dr. Lee Rosen (David Strathairn) and his team of Alphas, extraordinary individuals who can stretch the capabilities of the human mind, investigate an implausible murder at the behest of the Department of Defense. After determining that the assailant is completely unaware of his muderous action, they quickly realize a powerful group of extremist Alphas, known as Red Flag, is working against them. While incorporating a new member into their quirky fold, our team of Alphas must stop Red Flag and prevent the killing of the next target -- one of their own.

Marcus escapes from Binghamton causing Rosen to re-evaluate his feelings about the government.

The team relocates to new offices and investigates violent public riots.

On the trail of the Red Flag leader who ordered their assassination, the team discover a woman who cannot speak, but understands every known language.

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.

Gary and Harken come across an active FBI case involving a kidnapping; Hicks and Nina grow close after Nina is questioned about the death of her boyfriend.