The Season Two opener, "Red Rain," continues the action from last season's finale when Anna unleashed Red Sky on the planet. With the world on the brink of war and chaos all around, is there anyone who can stand up to Anna? Meanwhile, Ryan has been kept in isolation on the mothership, away from his hybrid baby so that Anna can experiment on her. Chad, seeking redemption for being used by Anna, now wants to fight with the Fifth Column, and Erica goes on a journey to find a scientist who can give her the answers to what Red Sky is, and where she learns the horrifying secret of what the Vs are doing on our planet.

Anna and Diana square off in the dark bowels of the Mothership – Diana has been down there for 15 years and not had a single glimpse of Anna. Meanwhile, Erica has Tyler's blood analyzed, and learns the Vs did something sinister to her when she was pregnant with him.

Erica learns her partner, Malik, is a Visitor and must fight for her life – literally – to stop Anna from finding out she's Fifth Column. Meanwhile, Anna learns that Malik is missing and orders Ryan to find her, while Lisa realizes her body is beginning to change, causing her to become more and more like her mother.