Dr. Molly Caffrey (Carla Gugino) is a contingency analyst whose job is to devise response plans for worst-case scenarios, including threats to national security. In a single instant, her life changes when one of those plans — "Threshold" — is activated by Deputy National Security Advisor J.T. Baylock (Charles S. Dutton).

Armed only with her hypothetical strategy to address an unprecedented occurrence — the appearance of alien life on Earth — Caffrey is thrust into a global crisis when an extraterrestrial craft is discovered in the Atlantic Ocean. Molly hand-picks a team of specialists, known as the Red Team, to help implement her plan: Dr. Nigel Fenway (Brent Spiner), a disillusioned NASA forensic microbiologist; Lucas Pegg (Rob Benedict), a brilliant but neurotic astronautical engineer; Arthur Ramsey (Peter Dinklage), a womanizing linguist and mathematician; and Cavennaugh (Brian Van Holt), a highly trained covert operative with a mysterious past.

Molly and her Red Team race against the clock and risk their lives to discover the purpose of the alien craft, determine what happened to the crew of the Navy vessel which discovered it, and prepare for what might be a full-scale alien invasion.