Molly and Cavennaugh go to a town called Allenville in search of a doctor who they think is infected and find more than they were looking for. Meanwhile, the situation at Threshold becomes heated with the pregnancy of the infected woman coming to an end.
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 using their heightened brain waves.
Lucas is infected with the alien DNA from something he ate. The infectees have harvested crops with the alien DNA. Caffrey must find a way to stop what could be nearly 200 new infectees. Also, one of the aliens approaches her with an interesting revelation.
Molly and Baylock realize the Threshold detainees must be moved immediately to a more secure facility in West Virginia after a prisoner attacks and infects a security guard, then tries to break himself and other infected prisoners out of their cells.
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.
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.
A patient at a 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 members might be involved.
Gunneson appears in Caffrey's house. Meanwhile, Lucas, Nigel and Ramsey try to figure out how the alien signals and DNA operate, and they come up with some interesting theories. Cavennaugh's team tries to locate Gunneson's other shipmates.
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 Adviser, J.T. Baylock, to investigate the incident along with a special scientific team of her choosing.
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