A mysterious alien object attacks a Naval ship and crew. Dr. Molly Anne Caffrey, a government contingency analyst, is contacted by the Deputy National Security Advisor, J.T. Baylock, to investigate the incident along with a special scientific team of her choice.

Gunneson reappears in Caffrey's house. Meanwhile, Lucas, Nigel and Ramsey try to break down how the alien signals and DNA operate and come up with some interesting theories. Cavennaugh's team tries to locate Gunneson other shipmates.

When a man at a fast-food restaurant is found with his head imploded, Molly and her Red Team investigate and begin to suspect the involvement of a group of military cadets, and the discovery that the infection has spread beyond the original Big Horn crew.

A patient at an psychiatric hospital in Ohio escapes and Molly believes he may have been infected by the alien signal after paintings of glass trees are found in his cell. After further investigation, it is suspected one of the missing Big Horn crew might be involved.

After a shipyard gang bust, a suspected fugitive Big Horn crewmember kills a police detective. Molly and Cavennaugh go undercover as Homeland Security agents. Unbeknownst to them, the real Homeland Security department is on the case.

As the signal from the Big Horn invades a Miami rave, the team investigates who have been infected, trying to prevent the signal from spreading to the population.

Molly and Cavennaugh investigate a newspaper leak regarding the Threshold program which might turn out to be an inside job. The Red Team look into a case of residents of a small town dreaming of trees made of glass.

Molly and Cavennaugh discover some strange happenings in a missing Big Horn crew member's hometown when they investigate the disappearance of a Threshold field agent.

When three women from completely different walks of life appear to be infected, Molly and the Red Team discover the connection among them and must locate the common cause.

Molly and Baylock realize the Threshold detainees must be moved immediately to a more secure facility in West Virginia when a prisoner attacks and infects a security guard, then tries to break himself and other infected prisoners out of their cells.

When a number of infectees and seemingly innocent people are killed, it becomes apparent that someone is going after people affected by the alien signal, and is locating them via their heightened brain waves. How is the killer linked to Bighorn crewman Manning, and does his method of finding his victims mean that Molly, Cavennaugh or Lucas could be next on his list?

Molly Caffrey and Cavennaugh go out to a town call Allenville in search of a Doctor who they think is infected and find more then they were looking for.

Meanwhile things at threshold get heated with the pregnancy of the infected woman coming to an end.