1. Trees Made of Glass (1)  

First aired: 9/16/2005    Production Code: 101

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 choosing.

2. Trees Made of Glass (2)  

First aired: 9/16/2005    Production Code: 102

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's other shipmates.

3. Blood of the Children  

First aired: 9/23/2005    Production Code: 103

When a man at a fast-food restaurant is found with his head imploded, Molly and her Red Team investigate and begin to suspect the involvement of a group of military cadets.

4. The Burning  

First aired: 9/30/2005    Production Code: 104

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 might be involved.

5. Shock  

First aired: 10/7/2005    Production Code: 106

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.

6. Pulse  

First aired: 10/14/2005    Production Code: 105

As the signal from the Big Horn invades a Miami rave, the team investigates who have been infected, trying to prevent the signal from spreading to the population.

7. The Order  

First aired: 10/21/2005    Production Code: 107

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.

8. Revelations  

First aired: 11/4/2005    Production Code: 108

Molly and Cavennaugh discover some strange happenings in a missing Big Horn crew member's hometown when they investigate the disappearance of a Threshold field agent.

9. Progeny  

First aired: 11/22/2005    Production Code: 109

When three women from completely different walks of life appear to be infected, Molly and the Red Team discover the connection among them and must locate the common cause.

10. The Crossing  

Production Code: 110

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.

11. Outbreak (a.k.a. Escalation)  

Production Code: 111

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.

12. Vigilante  

Production Code: 112

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 via their heightened brain waves.

13. Alienville  

Production Code: 113

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.