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.

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.

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.