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A century before Captain Kirk's five-year mission, Jonathan Archer captains the United Earth ship Enterprise during the early years of Starfleet, leading up to the Earth-Romulan War and the formation of the Federation.

A team of experts are assembled after the U.S. Navy discovers an extra-terrestrial object briefly appeared near a ship in the Atlantic Ocean.

The men of Enterprise fall under the seductive control of three Orion women. Trip is the only male member of the crew not to succumb to the women.

The trail of an infected cook leads Dr. Caffrey and Agent Cavennaugh to a small Virginia town populated by the infected.

An incident at a fast-food restaurant leads the Threshold team to a military academy, and the discovery that the infection has spread beyond the original Big Horn crew.

As the Threshold team tracks down the source of an infection and another member succumbs to it, the team chaffs under the pressure of their jobs. It becomes clear that Threshold will have to expand substantially to contain the infection but tidbits of information begin to suggest they may be fighting for the wrong outcome.

The Red Team traces the infection of three women to a fertility clinic.

A Miami DJ poses a danger when she begins using part of the alien signal in her mixes, threatening the infection of thousands.

Caffrey and Cavennaugh follow a lead on an infectee to an Indiana town with a preacher relating visions of an alien landscape.

Dr. Caffrey finds herself dealing with the Baltimore police and Homeland Security in an effort to gain the transfer of a captured infectee.

The team pursues an escaped mental patient whose room is filled with the drawings of the glass trees from Caffrey, Cavennaugh, and Pegg's dreams.

An attempted breakout by the infected humans in Threshold custody leads to a plan to transport them to a more secure location.

While the Red Team investigates reports of people in a New England seaside village dreaming of the glass trees, Caffrey tracks down a leak and deals with a senator's inquiries.

Worst case scenario expert, Dr. Caffrey, recruits a team of elite and slightly eccentric scientists to determine if an alien civilization has made first contact with the human race. Mysteries abound. Is the alien race trans-dimensional? Is it friendly or malevolent? If friendly, why did the crew members of the ship that encountered the alien kill each other? Is the strange helical symbol an attempt at communication? Are the aliens altering the DNA of human test subjects? And how are the odd dreams/nightmares everyone is having related?

At least one, and possibly seven, individuals from the ill fated Big Horn have survived but have disappeared. One in particular tends to reappear to menace but also possibly to communicate with Dr. Caffrey, then vanish just as suddenly. The team plans to capture the missing sailors with an audio segment from a video of the alien encounter which attracts rats found on the Big Horn. But with such limited testing there is no telling who, or what, might show up.

Arthur is busy with a stripper when an infected serial killer walks in on the scene kills the stripper but lets Arthur go untouched. WHY? Is this some higher Alien plot?