A V soldier is still on the hunt for Val when her water breaks and her baby will soon be born. Meanwhile, Erica, tired of being on the defensive, decides to go on the offensive and gets herself and Tyler invited up to the Mothership for a get-to-know-everyone-better dinner. But she has more than food on her mind; she's really there to find Anna's soldiers and destroy them. Meanwhile, after Father Jack asks Chad to help get a message to Joshua, he discovers that Anna's been using him.

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.

Erica, seeking revenge against Anna, heads to Hong Kong to carry out a mission to strike a lethal blow against Anna. Meanwhile, Anna learns that Tyler's phosphorous level is too low – even after the Red Rain – and he might become useless to her; and Lisa and Diana bond, beginning to form an alliance against Anna.

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.

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.

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.

Erica, now officially in charge of the global Fifth Column, leads them in a high risk attack against Anna. Anna meanwhile, growing closer in her plan to destroy humanity, finds a major obstacle in a certain Live Aboard candidate; and Ryan sneaks back onto the Mothership to try and rescue his daughter.

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.

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".

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.

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.

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.

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 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.