Dr. Rosen and his team must decide who to trust when Red Flag, led by Stanton Parish, escalates the war on the Department of Defense.

When a member of the team is suspected of being an agent for Red Flag, Dr. Rosen and the Alphas are abducted and held against their will in the Binghamton facility until the traitor is revealed.

The team finds themselves under siege by an undetectable Alpha.

Hicks and Nina fall under the spell of Jonas, an Alpha and charismatic cult leader willing to lead his followers to their deaths.

Agent Sullivan charges Dr. Rosen and the Alphas team with tracking down and protecting Skylar, an Alpha and technology whiz with a penchant for amazing inventions which, in the wrong hands, could prove highly dangerous.

Bill and Gary pursue an outside case, putting their Alpha powers to the ultimate test.

As Rachel returns home from her first date with new suitor, their first kiss overloads her senses. Back at the office, Dr. Rosen and his team of Alphas become official members of the Defense Criminal Investigation Service.

Moving in on a Red Flag stranglehold, Dr. Rosen and his team encounter a group of Alphas with unfathomable abilities. After they escape capture, Gary connects with their prisoner, Anna.

The team of Alphas, including new member Hicks, relocates to new offices in Queens after the attack on Dr. Rosen's life. While adjusting to their new surroundings the team investigates a series of violent public riots that are breaking out on the east coast. The only connection between the riots is a runaway teen, an Alpha, who overproduces certain pheromones that causes people nearby to become violent. Rosen's team must find a way to stop this Alpha without losing control themselves.

Marcus, a former patient of Dr. Rosen's with the ability to set off a chain reaction of events with a predetermined outcome, escapes from Binghamton, a facility designed to detain and train Alphas.

Dr. Lee Rosen and his team of Alphas, extraordinary individuals who can stretch the capabilities of the human mind, investigate an implausible murder at the behest of the Department of Defense.