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.

Chad reports from the Peace Ambassador Center as 100 diplomatic visas are being issued to the first wave of American Visitors, with Anna getting the first, but not everyone agrees with the decision. Erica has been tasked to protect the Vs and is tracking a death threat while paired with a V officer. Meanwhile, Ryan starts reaching out to his old friends to build up opposition forces and help fight the Vs.

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, Father Jack and Hobbes realize that the Vs know names and addresses of The Fifth Column members and must take drastic measures to protect them, while Ryan finally reveals to Val that he's a Visitor. Chad, with the camera rolling for "Prime Focus", begins the process aboard the Mothership's Medical Bay to have his aneurysm removed.

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.

After the radical faction of the Fifth Column murders three Peace Ambassadors, Erica goes on a mission to hunt down their leader, Eli Cohn, a former Mossad agent. Meanwhile, as Jack and other priests around the globe begin to speak out against the Visitors, Anna heads to the Vatican in an effort to convince the leaders of organized religion that the Visitors truly are "of peace".

Anna uses her newest gift to mankind, "Concordia," as a cover to hide an invading fleet of breeding vessels that will be used to ensure the perpetuation of Visitors for future generations. Meanwhile, Eli Cohn (guest star Oded Fehr) tries to convince Erica and the Fifth Column that the "Concordia" gala is the perfect time to assassinate Anna.

Anna, enraged at the increasing audacity of the Fifth Column attacks, enlists Ryan in an attempt to wipe out the Fifth Column in one fell swoop. Meanwhile, Father Travis, following Vatican orders, asks Jack to leave the church, and Lisa meets Diana, her grandmother – who Anna said was dead – for the first time.

Anna is about to pull the switch on the planet's first Blue Energy reactor, but Sid realizes that the size of the reactor is much too large for just the various Concordia sites – the Fifth Column needs to figure out what Anna is really up to. Diana tells Lisa she must act against Anna now, fulfil her destiny and save humans from annihilation.

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.