The team starts the day with a bang—chasing a man with a backpack through the busy streets of Manhattan in order to retrieve something from him that the Department of Defense wants badly. Thanks to some fancy footwork by Hicks and a well-timed push by Nina, the team succeeds, but unfortunately Gary is arrested.
Bill, who is having a rough day because he just found out the FBI is letting him go, volunteers to pick Gary up from the precinct. While he's there, Bill finds out about a high profile kidnapping that Gary has already intercepted some info about. Sensing an opportunity to work his way back into the FBI, Bill makes certain that he and his new "partner" Gary, or Agent Bell, are invited into the inner circle of the investigation.
Meanwhile, back at Alpha headquarters, Nina has problems of her own—A persistent detective who thinks she killed someone. Hicks wants to help her out but, in the process of giving her advice, the two of them feel some chemistry and start making out. Unfortunately, Rachel walks in on them, which breaks up the mood and the moment, but Nina does take the advice Hicks gives her and clears the slate with the police.
As the kidnapping unfolds, Bill and Gary meet the rest of the team working the case, including the victim's father and Sarah Nelson, his chief of security. Although the kidnapping looks like the work of a dangerous terrorist group, the FBI isn't interested in any help from the DOD, and especially not from Bill.
Undeterred, Bill forges ahead with Gary, keeping the rest of the Alpha team in the dark, at least until an attempt to acquire a suspect at a local bar results in flying bullets and Gary is hurt. Dr. Rosen is livid but now that Bill thinks that the kidnappers aren't professionals, he convinces Rosen to bring the whole team into the fray.
The team decides to nab the kidnappers before the ransom is exchanged in order to have the best chance of keeping the kidnap victim alive. As they monitor the situation from afar, they find out that Agent Persky, the FBI agent whom Bill attacked, and Sara Nelson, the kidnap victim's head of security are making the ransom drop.
As Gary, Bill, and Hicks try to decipher the cryptic ransom instructions, the main kidnapper prepares to kill the victim. When the team notices that most of the kidnapping activity occurs in the west Village, they swoop in on a recently rented apartment, and barely avoid getting blown to bits.
As Persky and Nelson drive towards the drop, Nelson asks questions that arouse Persky's suspicions, so when Bill sends Persky a text explaining that the kidnappers have an inside man, Persky quickly puts two and two together but Nelson gets the drop on him. Luckily, Gary is able to trace Persky's cell phone so the team can capture Nelson, the mastermind of the whole kidnapping, and save the kidnap victim.
When Bill finally gets the chance to re-join the FBI, he surprises himself and his teammates by turning them down. Looks like grumpy Bill has found a new home with the DOD's Alpha Team.
Watch a sneak peek of the season finale of Alphas. Aired: 10/22.
An injured and increasingly desperate Doctor Rosen seeks a final confrontation with Stanton Parish. Guest Staring Summer Glau.