Ominous messages steer a man to a building's rooftop, where he executes an improbable shooting in the opener of the series following a team of people with extraordinary abilities who investigate crimes linked to others like them.

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.

During a raid against Red Flag an unknown Alpha is discovered. Gary bonds heavily with her while the rest of the team tries to define the extent of their enemies reach.

The alpha team rescues an alpha from a group of hooded thugs, then discover she is a former associate of Dr. Rosen who wants nothing to do with him.

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.

Dr. Rosen's alpha group is abducted by Nathan because he suspects one of them is a Red Flag conspirator.

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.