Mensagens sinistras levam um homem ao telhado de um prédio, onde ele executa um tiroteio improvável na abertura da série, seguindo uma equipe de pessoas com habilidades extraordinárias que investigam crimes ligados a outros como eles.

A problematic former patient of Rosen's escapes as Rosen is getting acquainted with his Department of Defense liaison, and the rest of the team tries to balance their normal lives with their work as Alphas.

The team moves to new offices following the attack on Rosen; violent riots break out on the east coast, which are linked to a runaway teen.

The Alpha team closes in on Red Flag and rescues an autistic woman, Anna, with the ability to translate any language. The team tries to figure out Red Flag’s plan while Gary bonds with Anna.

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.

While Bill and Gary take on a case of their own, Nina and Cameron grow closer.

The team is ordered to find and protect Skylar, an Alpha with skills that could be dangerous in the wrong hands.

Hicks and Nina are entranced by a deadly cult leader named Jonas.

The DoD imprisons Rosen and his team after they suspect that one of the members is a Red Flag traitor.

Rosen and his team find out about a secret red flag meeting. Things come to ahead for the team and the future is cloudy.