The Alphas pilot introduces us to a team of ordinary citizens whose brain anomalies imbue them with extraordinary mental and physical abilities. Taking the law into their own hands, the unlikely group, led by Dr. Lee Rosen (Strathairn), investigates cases that suggest other Alpha activity to uncover what the CIA, FBI and Pentagon have not been able, or willing, to solve. These gifted individuals must balance their quirky personalities and disparate backgrounds with their not always visible powers as they work to solve crimes, stop the ticking time bomb and save the world.
Dr. Lee Rosen (David Strathairn) 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.
Marcus, a former patient of Dr. Rosen's (David Strathairn) 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. His escape causes Rosen to reexamine his tenuous relationship with the government, while he's being forced to get acquainted with his new Department of Defense liaison, Agent Sullivan (guest star Valerie Cruz).
The team of Alphas, including new member Hicks (Warren Christie), relocates to new offices in Queens after the attack on Dr. Rosen's (David Strathairn) 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.
Moving in on a Red Flag stranglehold, Dr. Rosen (David Strathairn) and his team encounter a group of Alphas with unfathomable abilities. After they escape capture, Gary (Ryan Cartwright) connects with their prisoner, Anna, an autistic young woman with the ability to understand all languages. Using her abilities Anna helps Gary, Rosen and the team uncover that Red Flag is plotting a large-scale terrorist attack that might change the existence of Alphas as we know it.
As Rachel (Azita Ghanizada) returns home from her first date with new suitor, their first kiss overloads her senses. Back at the office, Dr. Rosen (David Strathairn) and his team of Alphas become official members of the Defense Criminal Investigation Service (DCIS) courtesy of Agent Sullivan (guest star Valerie Cruz). Their first assignment takes them to Pennsylvania where an outbreak of sudden deaths involving a local high school are suspected to be the work of an Alpha.
Bill and Gary pursue an outside case, putting their Alpha powers to the ultimate test. Featuring guest star Alaina Huffman.
Agent Sullivan (Valerie Cruz) charges Dr. Rosen (David Strathairn) and the Alphas team with tracking down and protecting Skylar (guest star Summer Glau), an Alpha and technology whiz with a penchant for amazing inventions which, in the wrong hands, could prove highly dangerous.
Hicks (Warren Christie) and Nina (Laura Mennell) fall under the spell of Jonas (guest star Garret Dillahunt) an Alpha and charismatic cult leader willing to lead his followers to their deaths.
The team finds themselves under siege by an undetectable Alpha. Guest starring Brent Spiner and Rebecca Mader.
When a member of the team is suspected of being an agent for Red Flag, Dr. Rosen (David Strathairn) and the Alphas are abducted and held against their will in the Binghamton facility until the traitor is revealed.
Dr. Rosen (David Strathairn) and his team must decide who to trust when Red Flag, led by Stanton Parish (guest star John Pyper-Ferguson), escalates the war on the Department of Defense.