When an orphaned "Sixer" girl comes to Terra Nova seeking asylum, Jim and Shannon are at odds if they can trust her; Mira plots to reclaim a valued possession; Taylor begins to suspect there is a traitor in his midst and Reynolds admits his feelings for Maddy.

When Elisabeth, Jim, Malcolm and Taylor investigate radio silence at a nearby scientific outpost, they discover an outbreak of a mysterious virus causing memory loss, paranoia and eventually death. The group must work together to find a cure before they lose their sanity and all of Terra Nova is infected.

A crashing meteor wipes out all technology and wreaks havoc on the colony. Meanwhile, Maddy and Reynolds are stuck out in the wilderness, Elisabeth and Skye work together to save a life and Taylor tries to prevent Mira and the "Sixers" from invading Terra Nova. Also, a mystery man makes his presence known.

The colony falls victim to its first murder, and Jim and Taylor must find the perpetrator. Also, Skye helps Josh find a way to get Kira, his girlfriend from 2149, to the past, while Elisabeth and Zoe race to help an unborn Ankylosaurus survive.

As Taylor searches for the "Sixer" mole within Terra Nova, Jim stumbles onto an old murder, for which Taylor is the prime suspect.

In a bleak future, a police raid on a family lands the father—a cop—in jail, and a chance for his family to get a fresh start on Terra Nova forces him to take drastic measures

Taylor and Mira must set aside their differences when they encounter a prehistoric enemy; Jim closes in on the mole.

When Terra Nova comes under attack from a legion of Pterosaurs, Jim and Taylor must find a way to save the colony before it's completely overtaken. Elisabeth discovers a former flame is also living in Terra Nova and may have been responsible for her recruitment. Syke tries to make Josh feel at home and Reynolds get protective of Maddy.

Maddy starts interning for the colony’s greatest scientist, and her life is put in danger when she discovers a terrible secret. Meanwhile, Josh makes a deal with the devil in order to solidify his plan to bring his girlfriend from the future to Terra Nova.

Lucas races to assemble the final pieces of his mystery device, in advance of the 11th Pilgrimage's arrival. Also, Jim and Taylor confront the colony's "Sixer" mole, Skye is reunited with a familiar face and Terra Nova prepares for war.

In the two-hour Season Finale, the 11th Pilgrimage arrives in Terra Nova and the mysterious Phoenix Group in 2149 makes its move to pillage the past with the help of Lucas and Mira. Meanwhile, Jim and Taylor team up in a last stand against the Phoenix Group, a colonist makes the ultimate sacrifice and a decision is made that will change life in Terra Nova forever.