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.
Agent Sullivan (guest star Valerie Cruz) credentials Dr. Rosen (David Strathairn) and his team as members of the Defense Criminal Investigation Service and their first case takes them to Pennsylvania where an outbreak of sudden deaths involving a local high school are suspected to be the work of an Alpha.
Dr, Rosen is forced to challenge his most cherished values when he encounters an alpha leading a personality cult who sincerely wants to create a paradise for all humanity, a dream his alpha ability may make possible. But as members of the alpha group fall under the cult leaders and he refuses to recognize he may be responsible for the illnesses among the cult members Dr. Rosen is forced to act... if he can.
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.
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.
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.
Rosen and his team travel to a remote village of Alphas to ask Skylar Adams to look into the function of the photo stimulator. But Parish has people in the village, and soon the lives of both Skylar and her daughter, Zoe, are in jeopardy.
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.
Kat goes undercover to investigate the source of a street drug that makes its user invincible, while Rosen works to confirm his suspicions about Dani's being an informant for Parish. Meanwhile, Hicks suspects that his son may be an Alpha.
It's Midnight Run, Alphas-style as Hicks and Kat transport a valuable Parish asset: a babbling, off-his-nuts memory sponge Alpha named Mitchell. Mitchell just might hold the strategic intel they need to stop Parish...if they can outrun and outwit Mitchell's seemingly indestructible Alpha "caretaker". Meawhile, Rosen is on his own hunt- for Parish' Achilles' Heel, a weak point to strike at. But Senator's Burton sudden presence in the Alphas office threatens to expose Rosen and Nina's own Achillles' Heel.