Nolan and Irisa are mysteriously rescued from their underground confinement just in time to discover that enemy forces are marching on the town of Defiance, which has fallen on hard times following the collapse of the gulanite mines. Meanwhile, Datak, Stahma and Rafe run into deadly complications on their quest to reunite their family; and Alak comes to realize just how unstable her mother-in-law is during their journey through the woods.

T'evgin comes to Defiance seeking his daughter, who Nolan and Amanda offer to release in exchange for some gulanite; at the same time, Alak and Pilar head off alone to protect the baby; and Datak and Stahma are threatened into helping Gen. Tak's assault.

Amanda negotiates with the Omec, a new alien race, for the future of Defiance; and the Tarrs return to find much changed and their loyalties tested between the humans, the Omec, and the Votanis Collective. Meanwhile, Nolan and Irisa encounter a survivor of Votanis Collective atrocities that can aid their first strike against Gen. Rahm Tak's oncoming army.

Nolan and Amanda are captured while excavating a buried weapons cache; Berlin investigates a Votanis Collective bombing in the heart of Defiance and sees an opportunity to get revenge on Irisa; Stahma's clandestine relationship with the mysterious Omec leader T'evgin takes a turn.

Amanda and Doc Yewll must enlist the Omec for help rescuing Nolan and Irisa, who have fallen into an unexpected and potentially fatal tour of their own past. Meanwhile, Datak and Stahma prepare a decisive move against Gen. Rahm Tak, leader of the Votanis Collective.

Nolan and Berlin pursue the Tarrs after their connection to the Votanis Collective is exposed; at the same time, Alak comes to grips with his future as a father.