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

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

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.

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

Rosen seeks a final confrontation with Alpha leader Stanton Parish.

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.

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.

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.

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.

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

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.

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.

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