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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.

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 works with new allies to uncover a biological threat they suspect the Visitors have been plotting. Aboard the mothership, Anna meets with a special guest, while managing the investigation into the murder of a V. Chad does a segment on the V Healing Centers demonstrating their amazing medical abilities, but finds himself conflicted by some of his findings.

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.

Anna introduces her pilot program to invite select groups of humans to stay on each of the 29 space ships. Ryan must deal with the fact that Valerie's pregnancy is wildly accelerated. Tyler learns a secret about his mom and one of the team makes a sacrifice to save Ryan.

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.