20 years after angels descended from heaven to lay waste to the human souls they felt God had favored over them, a reluctant "savior" must arise to protect Vega, the last remaining stronghold of humanity. The savior has more to fear than just angels, as the elites of this new society conspire to gain power for themselves.

Alex rejects his new role as the Chosen One, but then a sleeper threat in Vega forces him to spring into action and protect the ones he loves. Meanwhile, Michael meets with Gabriel one last time before the war between angels and mankind reignites; and Gen. Riesen and David Whele try to tie up loose ends.

Alex attempts to escape his responsibilities as the Chosen One by leaving Vega, but an encounter with Gabriel's forces leave him and Michael fighting for their lives. Meanwhile, Riesen goes too far in the name of security.

Alex begins his training with Michael, but soon after has a vision that causes him to go rogue during an Archangel Corps mission. Elsewhere, Claire goes out on a limb to protect Riesen, however she can't stop his long-held secrets from coming back to haunt him; and David makes a move to secure his power.

Alex takes on the not-so-easy task of trying to exorcise captive eight-balls of their angel possessors, and enlists Michael and Claire for help; David closes in on William's underground acolytes; at the same time, Riesen overturns David's plan to usurp power with a new alliance.

Alex is called upon by Michael to help prevent any further casualties after innocent higher angels turn up dead in Vega; at the same time, Gabriel causes tension by revealing a long-hidden secret; William "re-educates" his father; and Noma reignites an old flame.

In the Season 1 finale, the revelation of a higher angel's identity puts Alex and Michael at odds and Alex goes before the Senate to plead his case. Meanwhile, the marriage of Claire and William is followed by General Riesen's departure from Vega, Arika meets a delegation from Helena who bring with them shocking cargo, and Gabriel raises some suspicions with his so-called surrender.