Rosen and his team find out about a secret red flag meeting. Things come to ahead for the team and the future is cloudy.

Operating within the Defense Criminal Investigation Service of the U.S. Department of Defense and led by preeminent neurologist and psychiatrist Dr. Lee Rosen, an expert in Alpha phenomena, the team investigates cases that point to others with Alpha abilities. As they work against the clock to solve this new brand of crime, they must prevent their own personality differences and disparate backgrounds from interfering with their ultimate mission to catch the enemy.

While Bill and Gary take on a case of their own, Nina and Cameron grow closer.

On the hunt for a killer, the team realizes the search has lead him directly to them with a deadly consequences.

While the team tries to cope with Danielle's death, a mysterious woman drops a baby off at the office and Gary is strangely drawn to protecting it.

An Alpha loses his mind and kidnaps Rachel; the team loses touch with reality while trying to find Rachel.

Rosen enlists Skylar's help to decode Parish's Alpha technology and endangers her life and the life of her daughter.

Rosen discovers the identity of the mole; Kat tracks a mysterious new street drug that makes users temporarily invincible.

An investigation leads Harken and Hicks to go undercover in a secret, underground Alphas-only Fight Club.

Rosen kidnaps and interrogates an Alpha prisoner; Harken and Gary search for Skylar.

Hicks turns defector and begins working for Parish; the team uncovers a plot to cause a massive, deadly blackout.

Hicks and Kat transport a valuable Parish asset; Roland holds the strategic intel they need to stop Parish.

Rachel goes on a date that ends with a powerful kiss; Rosen's team officially joins the Defense Criminal Investigation Service, and their first case is to probe a series of deaths linked to a high school in Pennsylvania.

The episode starts 10 months after the events in "Original Sin" and circumstances have changed for the main characters (for some more than for others). Two of them are pretty different from the last time we saw them, and the team might be missing a member or two. Or more.

While investigating a string of crimes, the team realizes that they are looking for Nina, who had gone AWOL, and try to stop her before she hurts herself.

The team is confronted with evidence of Parish's evil agenda; a young Alpha reveals a deadly ability.

Rosen seeks a final confrontation with Alpha leader Stanton Parish.

The team finds themselves under siege by an undetectable Alpha when they bring in a potential Red Flag member for questioning.

The DoD imprisons Rosen and his team after they suspect that one of the members is a Red Flag traitor.

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.

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 ordered to find and protect Skylar, an Alpha with skills that could be dangerous in the wrong hands.

Hicks and Nina are entranced by a deadly cult leader named Jonas.

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.