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故事开始于一天早上，人们醒来发现城市上空悬浮着巨大的外星飞船。而从飞船中出来的外星人表示对地球人并无恶意，是为追求和平而来，并赠送了超出人们想象的先进科技。但友好的外星人的有意显然没有表面上看起来这般简单。国土安全局特工Erica Evans（Elizabeth Mitchell） 在追杀一起恐怖袭击的过程中，偶然发现了外星来客的真正目的。但当 Erica 四处奔走却惹来杀生之祸时才明白，真正的外星人早已经在不知不觉中渗入了人类社会的重要机构，也包括她供职的国土安全局，一时间敌友难辨。走投无路的她开始和“反外星人抵抗运动”组织暗中合作，并结识了抵抗运动的领袖 Jack Landry 神父(Joel Gretsch)和一个支持地球人的V星人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.
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.
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.
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.
