Earth was invaded by aliens. A human father's mind was "harvested" by the alien and assimilated his mind into an alien body. But the father's will resisted and it fought the other aliens trying to attack the pregnant mother. The mother gave birth, in the middle of a battlefield, and the kid was picked up by another man. Rose was born in the glow of alien blue light, which made her grow fast. Rose had powers, which she used to free all harvested minds inside alien bodies (called Pilots) and helped reunite families.Rose (Lindsey Morgan) leads the human fleet against the Armada, the Harvester mothership in orbit of the Moon. However, after breaking through the enemy lines, Rose freezes before she can fire and one of her ships is destroyed. With the Armada preparing to fire on Earth, Rose is forced to destroy one of her own ships when it gets into the crossfire, sacrificing thousands of her own men, but she succeeds in destroying the Armada. Wrecked with guilt, Rose vanishes following the battle while humanity rebuilds over the next five years, living alongside billions of freed Pilots (Blue eyes means under alien control, red light means free).Five years after the battle, Rose lives in a tent city near the ruins of London, avoiding resistance forces led by Leon (Jonathan Howard) searching for her and keeping the aging effects of her hybrid nature at bay with the help of hyper-oxygenated blood transfusions prepared for Rose by her friend Dr. Mal (Rhona Mitra). A viral pandemic strikes the Pilots and anyone using transplanted Pilot limbs such as Huana (Yayan Ruhian) who lost both of his arms and a leg while fighting against the aliens fifteen years before. The virus eats the Pilots alive while reverting them back into their brainwashed state (blue eyes). This means in 72 hours they will be back to ripping the brains out of humans.Leon captures Rose and brings her before General Radford (Alexander Siddig) who reveals that the Armada's core drive warped to the Harvester home world, Cobalt One, moments before Rose destroyed the ship. Only with the Armada's core drive do they have a chance of saving the Pilots. Core has enough power to transmit and control to all pilots. After being reunited with her Pilot adoptive brother Trent (Jeremy Fitzgerald), Rose reluctantly agrees to join the mission. Rose is concerned that Cobalt one is totally uncharted, and humans have no probes around the planet. So, they are flying in blind.At Cobalt One, the team's ship crashes after a collision with an empty Harvester vessel that leaves the ship running on emergency power. Rose, Trent, Leon, Owens (Daniel Bernhardt) and Alexi (Ieva Andrejevaite) find the planet filled with the bodies of dead Harvesters and strange shadow creatures that appear to be mutations of the Harvesters. Alexi is heavily wounded and sacrifices herself with a pulse grenade to kill the creatures, but the team manages to reach the Armada where Rose is briefly possessed by the Matriarch (Phong Giang), the Harvester leader who accuses the humans of coming to destroy her species.Trent follows her and helps Rose to break free of the Matriarch's control and Rose realizes that the Matriarch's telepathic influence was what caused her to freeze and her problems with her powers since. Now no longer afraid of who she is, Rose embraces her powers and steals the core drive. However, Owens betrays the others, infects Trent with the virus and flees with the core drive (Leaving Leon and Rose inside the Armada).Stealing an alien tanker in order to escape, Rose and Leon discover that Radford had bombed Cobalt One (in the form of a probe) prior to their arrival with a biological weapon, the same virus that is infecting the Pilots on Earth. As Rose and Leon make their way back aboard the ship, Radford uses the core drive to destroy Cobalt One and the Harvesters in an act of genocide. Confronted by Rose and Leon, Radford reveals that the virus was intended to peacefully euthanize the Pilots and to destroy the Harvesters, but it had the unintended side effect of reverting the Pilots back into their brainwashed state. Having boarded the ship as well, the Matriarch attacks, killing Radford and intending to destroy the Earth in revenge.Owens who is being checked on by Zhi (Cha-Lee Yoon) (The navigation expert who cracked the location of Cobalt one), attempts to attack Zhi after he realizes the truth about the virus, but Zhi manages to fight off Owens who attacks Leon and Rose. As the ship enters a wormhole, Owens falls into an energy field and is disintegrated while Trent, whom Leon manages to snap back to normal, knocks the Matriarch in as well, but has most of his body disintegrated in the process.On Earth, Mal works on a cure in the tent city, but the infected Pilots attack before she can finish testing it. The residents, including Mal, Kate (Naomi Tankel), Grant (James Cosmo) and a cured Huana, fight back and manage to eliminate the attacking Pilots at the cost of Grant and several others, only to have an army of thousands more approach from London. Arriving back in the nick of time, Rose sucks all of the Pilots into her ship and informs Mal that with Mal's cure and Rose's ship, they now have the power to cure all of the infected Pilots worldwide.In the aftermath, Mal transplants Trent's brain into a new Pilot body, saving him. Zhi hacks into Radford's personal files and discovers the location of a prison where Radford held anyone that he considered to be an enemy of the state, including Rose and Trent's long-missing father Mark Corley. Rose orders a course set for the prison, intending to rescue her adoptive father.