A grocery store clerk receives a mysterious call that puts him into a trance and sends him to a rooftop to shoot a Federal witness... through an air vent a block away. The government calls in Dr. Leigh Rosen and his team of "Alphas," people with special neurological abilities, to locate the killer.
An Alpha escapes the Compound en route to special treatment, and goes after Rosen, the man he believes had him locked up. Meanwhile, Rosen copes with his new DoD liaison and has second thoughts about his team's involvement with the government.
When an Alpha causes riots and deaths, the government calls in Rosen and his team to find the culprit and stop her before it's too late.
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.
The team is called in to investigate a series of deaths in a Pennsylvania town where the victims suffered from massive organ shutdown.
When a millionaire's daughter is kidnapped by a drug cartel, Bill sees a chance to get involved and guarantee his reinstatement with the FBI. But to crack the case he'll need Gary's help. Meanwhile, Cameron gives Nina some personal advice.
-- Cumbia de los Muertos
The team comes to the aid of a young Alpha wanted by the government due to her ability to create high-tech gadgets from common electronics. Meanwhile, Bill considers fatherhood and Gary fights with his mother over his job.
An Alpha uses his abilities to form a cult and takes control of Nina and Cameron. Meanwhile, Rachel tries to get her father to seek treatment for his incipient cancer.
After capturing an Alpha working as an obstetrician to cause an increase in Alpha births, the team returns to their office only to discover that they are under siege by an Alpha capable of avoiding any form of detection.
Nathan Cley captures the entire team and takes them to Binghamton, and informs them that one of their members is a traitor. Now the team must determine which one of them is a mole once they find a way to escape.
After a major confrontation between Red Flag and the DoD that ends in bloodshed for both sides, Rosen makes a drastic decision that will affect the fate of Alphas everywhere.