Taking place simultaneously with the events of Skyline, the story follows Mark Corley, a Los Angeles police detective who's desperately trying to reconnect with his estranged son, Trent. As Mark helps Trent escape from jail, a catastrophic alien invasion erupts, engulfing the entire city’s populace in mysterious blue light, pulling them into various alien spaceships. In the chaos, Mark must lead a small band of survivors through a network of underground subway tunnels, though tragically, many are picked off one by one.
Mark, Trent, the transit operator Audrey and a blind homeless man dubbed Sarge, manage to flee to the marina after the city is decimated in a nuclear explosion, only to find themselves abducted by a massive alien vessel. Aboard the ship, Mark embarks on a frantic search for his son, encountering another survivor, Elaine, and her husband Jarrod, who has been transformed into a bio-mechanical alien soldier, yet retained part of his human consciousness.
During their time together, Elaine goes into labor and, tragically, dies during childbirth, leaving Mark and Jarrod to forge a plan to obliterate the alien ship utilizing explosives. During an intense confrontation, Jarrod sacrifices himself, allowing Mark to rescue Audrey, though he is too late to save Trent, whose brain has been forcibly integrated into another alien machine.
As Sarge succumbs to his injuries after a valiant defense of the newborn, Mark, Audrey, and the baby narrowly escape a soon-to-be self-repairing spaceship. They serendipitously encounter Sua and his sister Kanya, members of a drug cartel, who are at odds with both the aliens and corrupt ex-police bandits.
Their journey through the treacherous jungle reveals something astonishing: the human baby is aging rapidly, transforming from an infant into a three-year-old in a mere day. With Sua and Kanya's guidance, they reach a concealed human resistance hideout nestled within local ruins, but their group faces a formidable obstacle when Huana, the rogue policeman leader, attempts to ambush them, only to be disarmed and captured.
Harper, a former drug chemist turned medical officer, examines the accelerated baby girl and realizes her unique DNA might hold the key to combating the alien threat. Harper devises a serum that could liberate the bio-mechanical soldiers from alien control. Despite Sua’s initial inclination to eliminate all transformed beings, Mark persuades him to help save Trent.
Meanwhile, Kanya’s heroic sacrifice to an alien creature leads to an unexpected peril, as their location is revealed to alien forces searching for the human infant. In the ensuing battle, many resistance fighters, including Harper, fall. Mark fights back using Harper’s serum to turn the mind-controlling blue light into a freeing red light, but chaos ensues as the alien leader launches a vicious attack.
In a desperate turnaround, Mark, Audrey, Sua, and Huana launch a counteroffensive against the alien hordes. Despite sustaining severe injuries, Huana fights valiantly alongside them. Just as Trent’s consciousness rekindles through his father's presence, he rallies aboard an alien tanker. In a climactic showdown, Trent vanquishes the alien leader and activates the serum, liberating the afflicted bio-mechanical soldiers.
With Earth rescued from alien dominion, Audrey names the girl Rose after Mark's departed wife. Fast forward ten years, Rose has transitioned into a commanding figure of an alien ship, with an alien-turned-human Trent as her steadfast second-in-command. Together, they undertake a mission against the remaining alien ships orbiting the Moon, seeking to reclaim their freedom.
