Plot
Ten years after the first invasion [a] , Rose leads the human fleet against the aliens, now called 'Harvesters', aboard the Armada, a mother ship orbiting the Moon. When she breaks through enemy lines, she hesitates to fire, one of her ships is destroyed. As the aliens prepare to attack Earth, Rose sacrifices another one of her ships, killing thousands, but ultimately destroys the Armada. Overcome with guilt, she vanishes while humanity rebuilds, coexisting with billions of 'Pilots', hybrid alien-humans.
Five years after the battle, Rose lives in a tent city near the ruins of London, avoiding resistance forces searching for her and keeping the aging effects of her hybrid nature at bay with the help of hyper-oxygenated blood transfusions prepared by her friend Dr. Mal. A viral pandemic strikes the Pilots and anyone using transplanted Pilot limbs. The virus eats the Pilots alive while reverting them back into their brainwashed state. Resistance leader Leon captures Rose and brings her before General Radford who reveals that the Armada's core drive warped to Cobalt One, the Harvester homeworld, before the ship's destruction. Only with the Armada's core drive can they save the Pilots. Rose reluctantly agrees to join the mission.
At Cobalt One, the ship crashes, leaving it on emergency power. Crew members Rose, Trent, Leon, Owens, and Alexi find a planet filled with dead Harvesters and strange mutations. Severely wounded, Alexi sacrifices herself with a grenade. The team reaches the 'Armada', where Rose briefly succumbs to the Harvester Matriarch's brainwashing, who accuses humans of wanting to destroy her species. Trent helps Rose break free, revealing that her telepathic influence caused her to freeze during the war. Now empowered, Rose steals the core drive. However, Owens betrays the team, infecting Trent and fleeing with the core drive.
Rose and Leon later discover that Radford bombed Cobalt One before their arrival with a biological weapon, the same virus that is infecting the Pilots on Earth. As the two return aboard the ship, Radford uses the core drive to destroy Cobalt One and the Harvesters in an act of genocide. He reveals to them that the virus was intended to peacefully euthanize the Pilots and destroy the Harvesters, but it had the unintended side effect of reverting the Pilots back into their brainwashed state. Having boarded the ship, the Matriarch also kills Radford, intending to destroy the Earth in revenge. After realizing the truth about the virus, Owens attacks Zhi, who manages to fight him off. As the ship enters a wormhole, Owens disintegrates into an energy field. Trent, whom Leon manages to snap back to normal, knocks the Matriarch in, but has most of his body disintegrated.
On Earth, Mal works on a cure, but infected Pilots attack before she can finish testing. The residents, including Mal, Kate, Grant, and Huana, fight back, eliminating the Pilots but losing Grant and others. Just in time, Rose arrives and sucks all the Pilots into her ship. With Mal's cure and her ship, they can now cure all 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 had 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.
