Eight months after last year's finale with the stage set for an explosive turn of events at the Binghamton facility (the Guantanamo of the Alpha world) that could have devastating, far-reaching consequences. Dr. Lee Rosen, having exposed the existence of Alphas to the unsuspecting public, finds himself discredited and imprisoned by a government desperate to cover up his revelation. The rest of the core team has disbanded and some, without Rosen's guidance and care, have regressed to their old, destructive ways. They must now battle their individual demons in order to reunite and try to save their own.
Rosen and his team look for an Alpha hugger, but the hunter becomes the prey when the Alpha comes after them.
An investigation leads Harken and Hicks to go undercover in a secret, underground Alphas-only Fight Club.
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.
An Alpha loses his mind and kidnaps Rachel while visiting the hospital.
Rosen enlists Skylar's help to decode Parish's Alpha technology and endangers her life and the life of her daughter.
Rosen and Parish face off against each other after a young Alphas emerges with the deadly ability to control minds.
Rosen discovers the identity of the mole; Kat tracks a mysterious new street drug that makes users temporarily invincible.
Hicks turns defector and begins working for Parish; the team uncovers a plot to cause a massive, deadly blackout.
Difficult times arise for the Rosen and his team as the loss of a loved one shocks everybody and forces them to change their way of handling Stanton Parish. However, they must put aside their worries when the life of one of the team is put in jeopardy.
Cat returns to the team as they set out to find Stanton's secret weapon... and protect him. Meanwhile, Senator Burton challenges Rosen's methods of fighting rogue Alphas.
An Alpha prisoner is kidnapped and interrogated by Rosen, who is still reeling from the death of his daughter; and Harken and Gary track down Skylar, but freeing her from Parish's clutches proves tricky.
A desperate and slightly delusional Rosen becomes determined to confront Stanton Parish over Dani's fate, while the team races against time to keep the Alpha leader's deadly plan from happening.