Taking place at the same time as Skyline, Mark Corley, a Los Angeles police detective, helps his estranged son, Trent, out of jail just as an alien invasion begins. The entire population of the city is sucked into various spaceships by a blue light. Mark leads a group of surviving humans through underground subway tunnels to escape, though most of the humans are killed or abducted, one by one. The survivors – Mark, Trent, transit operator Audrey, and a homeless man known only as "Sarge", who is immune to the blue light due to his blindness – escape to the marina following the city's nuclear destruction, only to be abducted into the alien flagship by a towering alien tanker. On board the spaceship, Mark tries to find his son and storms his way into various chambers, where he meets up with survivor Elaine and her transformed husband Jarrod (from the first film). Elaine explains that Jarrod retained control of his mind despite being transformed into a bio-mechanical alien soldier. Though Elaine is three months pregnant, her pregnancy has accelerated and she gives birth to a daughter. Elaine dies during the delivery, and Mark and Jarrod team up to destroy the alien ship by setting alien explosives inside the ship's control systems. When Jarrod is killed fighting the alien leader, Mark rescues Audrey but is too late to save his son. Trent has his brain taken and placed in another alien bio-mechanical machine creature. Sarge is badly wounded when he defends the baby from an alien. The dying Jarrod destroys the ship, which crashes in rural Laos.