After a violent attack on someone very close to Anna, she delivers a message that the Vs don't feel safe and will be leaving, while she also gives a list of possible Fifth Column members to Chad hoping he'll investigate to help in finding them. Meanwhile, Erica and the team try to track down a scientist who may have created a weapon that the Visitors are afraid of.

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 is focused on having Lisa breed with Tyler to ensure the evolution of the Visitors, while Erica and Diana enlist Lisa to stage a coup against Anna and remove her from power before humanity is destroyed. Erica and the Fifth Column join Lisa in the attempted coup, which has devastating results. Also in the episode, Marc Singer, who played freedom fighter Mike Donovan on the original "V" series, guest stars as Lars Tremont, a member of a top secret organization of high-ranking military and government leaders from around the globe who have long suspected that the Visitors are very much not here in peace.