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.
A visiting arms dealer changes Defiance's fortunes, and divides Amanda, Nolan and Berlin; at the same time, Nolan encounters difficulty recruiting a militia to fight the oncoming Votanis Collective army. Elsewhere, Stahma's presence causes strife among the mysterious Omec; and Datak and Alak have a reckoning.
Defiance is under siege. As Nolan, Amanda, Irisa and the militia defend the town against the Votanis Collective, Datak recalls his father's chilling lessons and makes a pivotal decision, while Stahma takes an unexpected trip.
A gruesome hug is committed by an unusual beast that's on the loose and being hunted down by Nolan and Irisa, while Doc Yewll delves into the surprising victim. Elsewhere, Amanda resists welcoming back Stahma; and T'evgin learns an unsettling truth about his daughter.
Amanda decides to ignore Nolan's skepticism and welcome an encouraging Votanis Collective delegation to Defiance. Meanwhile, Stahma's loyalties are tested by an unexpected arrival; and T'evgin takes another step towards acclimating to life on Earth.
Kindzi frees Nolan from the VC as they take him to South America for trial, rather than let him die at the hands of her enemies. However, Irisa and Berlin track her down and demand answers. Meanwhile, Yewll continues "collecting" people for Kindzi, and Stahma discusses wedding plans with Andina.
Nolan, Amanda and Irisa search for a way to stop invulnerable Kindzi from waking and transporting more Omec to Earth; Datak seeks escape from a deadly compound; and Stahma implores Alak for forgiveness before it's too late.
Omec hunts Defiance citizens; Nolan, Amanda, and the others undertake a potential suicide mission to end the threat once and for all.