Seven strangers wake up in a seemingly empty small town where they are under constant electronic surveillance. Implants keep them from leaving the town borders, and they have no choice but to figure out why they were abducted and what ties them together. Meanwhile, a reporter tries to locate one of the missing persons.
Moira removes the implant device in everyone's thigh hoping that will allow them to escape. Also, Joe and McNair try to learn more about the invisible fence. Meanwhile, reporter Renbe tries to find more out on Janet's disappearance, but he doesn't get any leads.
A helicopter appears above the hostages, but it turns out it is only there to provide them with a box.
Nerves are rattled when the night manager informs the group that someone will be "checking out." The tension mounts when a taxi arrives with instructions to take Janet and the guest of her choice. After being left behind, Tori makes a plea to the camera to be set free and a second taxi arrives to take her. Meanwhile, Joe pays a surprising visit to someone in town
After discovering that Tori is missing, the group's search for her turns up a mysterious newcomer with the name "Erika" tattooed on her arm. Erika reacts unhappyly to her new surroundings and physically attacks Joe, Janet, Blackham, and Moira. Meanwhile, a suspicious Renbe believes he's found a link between Tori's fate and Janet's disappearance.
When Joe suddenly falls unhappyly ill, the group becomes alarmed. Meanwhile Erika discovers an antidote, but refuses to give it to Joe unless he comes clean about his secret. Elsewhere, reporter Renbe and Kat attend Tori's funeral in Rome and discover that her father, the U.S. ambassador to Italy, is also investigating her disappearance.
Joe puts himself into a vulnerable position when he confesses everything he knows about the kidnappers and their organization to Janet; Kat, Renbe and Stefano are certain that Joe is the key to finding Tori and Janet.
Joe, Graham, and Bill are forced to confront their pasts. Meanwhile, Renbe and Kat try to find the one person who escaped the program.
Joe returns to the town, but claims to be suffering from amnesia with no memory of his fellow prisoners. They discuss what to do with him, while at Program headquarters, the Director reconsiders her approach. Meanwhile, Kat and Renbe try to escape San Nicasio and find an answer to many of their questions.
The new night manager lays down the law, locking everyone into the hotel. Meanwhile, Kat and Renbe's quest takes them to an abandoned duplicate of the town.
Unable to trust Joe, Janet sets her sights on Ulrich as her ticket out of town. Morse and Blackam begin to take ease with Ulrich due to his nice personality and helpfulness, but soon realize his true intentions. Meanwhile, Kat and Renbe have returned to San Francisco, only to find out that their lives in America have been severely changed by "The Program".
The seven captives discover that all of the supplies have disappeared, but their captors have left them six body bags. Joe and Ulrich explain that they are expected to fight among themselves, and only one will survive. Meanwhile, Kat and Renbe discover another Program survivor, who insists that he was never a captive and claims to have no idea what they're talking about. And Ulrich lets his feelings overwhelm him and loses his head over Janet.
After surviving an unexpected van crash, the abductees finally escape and decide to go their separate ways. Everyone attempts to return to their normal lives, however, "The Program" has no intention of letting them go. Meanwhile, Renbe and Kat race to help Janet, only to end up reunited with the rest of the group in eerily familiar territory.