After Claire drops a bomb on Gabriel's mountain fortress Alex and Noma are freed, and set out on the road to New Delphi. Meanwhile Michael, now living in isolation, discovers a small town of humans who have inexplicably managed to survive the war and the demon occupation of Earth.
Alex and Noma attempt to persuade the leader of New Delphi to forge an alliance with Vega, while Gabriel tries to recapture his quarry. Following an assassination attempt Claire uses an 8-ball to gain leverage over David, and in a remote village Michael attempts to keep his secret.
Alex enters an isolated part of Vega to prove his worth to the city's leader, only to find a familiar face. Michael learns that his friend is about to make a great sacrifice, and Claire hires someone to search for an escaped prisoner -- anticipating a full-scale revolution from the V1s.
Alex and Noma discover New Delphi's terrifying secret, exposing Julian's plans against the archangels. In Vega, David Whele is captured by the V1s and tries to negotiate for his life, and Claire and Gates are besieged by an angel assassin.
Michael and Gabriel go to New Delphi together, where Alex plans to help Julian capture one of the higher angels. After Claire puts pressure on Zoe and the V1s by putting a bounty on her head, David negotiates on behalf of his captors.
While Alex goes in search of Michael, Julian exacts a cruel vengeance on Gabriel and interrogates Noma for information. Meanwhile David tries to make Zoe into the leader of a revolution as Vega descends into civil war, and Gates goes behind enemy lines to shut down a radio broadcast.
Julian subjects Gabriel and Michael to torture, prompting them to remember a time when Gabriel was a different man. Desperate for supplies to help Noma, Alex brings her to a store where 8-balls are living, and back in Vega Claire tries to get Zoe to come to the negotiating table.
Julian uses General Riesen's lost love to try and manipulate information out of him. Claire plans her next move against the rebels, leading to a violent showdown. Meanwhile, William Whele -- long believed to be dead -- walks back into Vega.
On their way back to Vega Michael, Alex, and Noma stumble upon an 8-ball army in stasis. Julian subjects Michael to a toxin with divine origins, and Gates received an ultimatum from Claire's prisoner. As the streets of Vega are consumed by civil war, David comes face-to-face with his son.
Alex and Gates must work together after the rebels seize control of Vega's nuclear reactor, which is soon on the verge of a catastrophic meltdown. Michael must face the repercussions of his time in Mallory when he is confronted by the Prophet, and General Riesen comes face-to-face with Gabriel.
Vega is consumed by the Darkness, a weapon that brings out humans' deepest nightmares. While Michael leads a mission to eliminate the weapon Claire imagines her child, William struggles with the truth about his time in the desert, and Arika finds herself at the receiving end of her own manipulations. Meanwhile, David encounters a monstrous version of himself.
In the wake of the Darkness Julian's 8-ball army moves to attack Vega, and Alex and Noma try to rally a militia to fend off the horde. Claire faces David once again, and Michael and Gabriel's long-standing differences reach a boiling point.
Gabriel brings Michael back to the town of Mallory, where he believes they may find the brother they believed to be dead. The people of Vega fight to save their city from the 8-ball army, and Alex and Claire are reunited under tense circumstances. Twenty-five years in the past, Noma's dark secret is revealed.
