Chad Decker hosts a debate about the Vs. Suspicion arises from FBI investigator Erica who believes that the Vs have different intentions to what they claim. Erica and Father Jack find themselves being tracked down by a seeker.

Erica finds her life in danger when she's attacked at home. A dangerous new member is recruited for the Resistance as the Visitors shore up their defenses. Anna wonders why Chad hasn't followed up on his diagnosed aneurysm and Ryan's concern grows over Val's "abnormal" pregnancy.

Chad and Anna are in Geneva for the U.N. Energy Summit where Anna is going to present a gift of technology to the world. Meanwhile, Erica learns that the V Task Force is investigating The Fifth Column. Valerie goes on the run, knowing something is different about her baby and not sure she can trust Ryan.

Erica, Ryan, Father Jack and Hobbes learn Anna's sent a V shuttle filled with a deadly tracker team to find them, and must figure out how to stop the shuttle from landing. Meanwhile, Anna gives Tyler his invitation to the Live Aboard Program and Chad confronts Father Jack on what he knows about The Fifth Column.

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 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.