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.

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.

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.

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.