When a grocery clerk commits an impossible assassination, the government calls in Dr. Leigh Rosen and his team of "Alphas": unique individuals with neurological mutations that give them special abilities. The team must determine who the killer is and track him down, but soon discover that a greater plan is in motion.
Rosen tries to cope with his Department of Defense liaison and a former Alpha patient with the ability to understand causality who wants him dead... or does he?
The team deals with a runaway teenage Alpha setting off riots up and down the East Coast. Meanwhile, Rosen discovers that the government isn't so willing to cooperate with him as he believed.
While trying to thwart a Red Flag operation, Rosen and his team find a captive woman, Anna, who can translate any language. While the others try to track down the Red Flag leader, Gary bonds with Anna over their similar conditions.
A young Alpha with the ability to create powerful inventions from common items goes missing, and Rosen and his team are called upon to find her... and protect her. Meanwhile, Gary challenges his mother and Bill contemplates fatherhood.
After capturing an Alpha working as an obstetrician, the team takes on an Alpha with the ability to remain unseen and undetectable against any opponent.
Rosen and his team must choose sides when the DoD launches a full-out assault on Red Flag. Rosen reunites with his daughter Danielle, who was being hunted by Red Flag.