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Dozens of UFOs suddenly appear on Earth, hovering over major cities around the world and claim that their objective is to help the Human race, providing vastly superior intelligence and technology in exchange for water and minerals only found on Earth. The leader of the Vs, Anna, uses popular TV anchor Chad Decker to deliver her messages to the Humans, but suspicion arises from FBI investigator Erica who believes that the Vs have different intentions to what they claim.

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.