Dr. Rosen (David Strathairn) and his team must decide who to trust when Red Flag, led by Stanton Parish (guest star John Pyper-Ferguson), escalates the war on the Department of Defense.
Separated from the team and haunted by vivid hallucinations of his daughter, Dani, an injured and increasingly desperate Doctor Rosen seeks a final confrontation with Alpha leader Stanton Parish.
As the Alpha team attempts to interrogate an alpha doctor, who wants to create more alphas, an invisible alpha attempts to abduct him. Dr. Rosen struggles to determine who is the more dangerous.
The alphas rescue Dr. Rosen's estranged alpha daughter from an assassin. She carries a carefully coded message stolen from Red Flag. But Dr. Rosen suspects it's a ruse which leads him to take precipitous action.
The Team investigates an Alpha-related crime spree leading to one of their own, who is in the midst of a dangerous emotional breakdown. Our Team races to stop them before they hurt themself or someone else.
An investigation leads Harken and Hicks to go undercover in a secret, underground Alphas-only Fight Club where they meet "Kat", an energetic fellow Alpha whose can instantly memorize any physical or mental skill.
When Jason Miller returns to school, he uses his newly-enhanced Alpha ability to form a neural network of classmates who bend to his will. Rosen begrudgingly agrees to team up with Stanton Parish to get Jason to release his mind slaves.
When Hicks turns defector and beginning working for Parish, Rosen and the team can only wonder: has Hicks truly turned, or is he playing a deeper game involving Dani?