1.01 – Trees Made of Glass: Part 1 (aired on September 16, 2005)
Directed by David S. Goyer | Written by Bragi F. Schut

Dr Molly Caffrey is a contingency analyst who deals in worst-case scenarios. When a mysterious light in the sky has a fatal effect on a ship’s crew, it’s time to implement `Operation Threshold’. A mysterious alien object attacks a Naval ship and crew.

1.02 – Trees Made of Glass: Part 2 (aired on September 16, 2005)
Directed by Peter Hyams | Written by Bragi F. Schut, David S. Goyer

An eerie light in the sky has a deadly effect on all who see it. It’s time to fear the worst: they’re out there, and they’re out to kill.

1.03 – Blood of the Children (aired on September 23, 2005)
Directed by Bill Eagles | Written by Anne McGrail

When a man at a fast-food restaurant is murdered, Molly and the Red Team investigate and begin to suspect the involvement of a group of military cadets.

1.04 – The Burning (aired on September 30, 2005)
Directed by John Showalter | Written by Brannon Braga, Dan O’Shannon

A routine search for an escaped psychiatric patient becomes a mystery when Molly and the Red Team learn the patient has the same dreams as Caffrey, Cavennaugh and Pegg.

1.05 – Shock (aired on October 7, 2005)
Directed by Tim Matheson | Written by André Bormanis

Molly and the Red Team suspect that one (Xaypani Baccam) of the missing Big Horn crew members is involved when a police officer dies during an arrest.

1.06 – Pulse (aired on October 14, 2005)
Directed by Bill L. Norton | Written by Mike Sussman

A Miami DJ becomes infected with the signal and begins incorporating it into her music; Molly and the team must find her before she spreads it to her audience.

1.07 – The Order (aired on October 21, 2005)
Directed by Norberto Barba | Written by Anne McGrail

Molly investigates a security leak that could put the entire Threshold plan in jeopardy; the Red Team probes a possible infection of a local food supply in a New England town.

1.08 – Revelations (aired on November 4, 2005)
Directed by Thomas J. Wright | Written by Amy Berg, Andrew Colville

Molly and Cavennaugh keep a suspicious eye on a local preacher (James Frain) who captivates his parishioners with his visions of a sea of glass and the impending apocalypse.

1.09 – Progeny (aired on November 22, 2005)
Directed by David Jackson | Written by Barbara Nance

Three women from completely different walks of life show signs of being infected, leaving Molly and the team to try to find the common thread and stop the spread of contamination.

1.10 – The Crossing (aired on January 11, 2006)
Directed by Paul Shapiro | Written by Bragi F. Schut

An attempt to transport infected detainees to a holding area is endangered when the convoy is attacked, and Molly faces a dilemma when a Threshold guard is infected.

1.11 – Outbreak (aired on January 18, 2006)
Directed by Felix Alcalá | Written by Dan O’Shannon

Caffrey must find a way to stop 200 new infectees of the alien DNA. One of the aliens approaches her with an interesting revelation.

1.12 – Vigilante (aired on January 25, 2006)
Directed by Felix AlcaláJohn Showalter | Written by Mike Sussman

A doctor launches a crusade to murder infectees, but he puts ordinary people at great risk. Meanwhile, Ramsey’s decadent lifestyle puts him in close contact with the infection.

1.13 – Alienville (aired on February 1, 2006)
Directed by Oz Scott | Written by Anne McGrail

Molly and Cavennaugh search for a doctor who may be infected; the pregnancy of an infected woman comes to an end.