In the same time where the first film left off, Mark Corley is a Los Angeles police detective who visits his estranged teenage son, Trent, just as the alien invasion begins and the entire population of the city is sucked into the various spaceships by the blue light. Mark storms his way onto one of the alien ships to rescue his son, where he meets up with Elaine and her transformed alien husband, Jarrod, to battle the aliens and protect a newborn daughter.
However, it was too late to save Trent from having his brain taken. Jarrod and Mark attempts to destroy the ship by setting explosives inside. After blowing up the ship and Jarrod died, the alien ship crashes in Southeast Asia, where Mark must forge an alliance with a band of survivors. Unaware to Mark, Trent’s brain was placed into an alien.
They discover the key to turn all aliens’ eyes into red and return their brains to normal to save everyone. During the fight at night, Mark entered a ship, where he uses the red bomb to turn blue into red lights, and turning his “alien” son to red and restoring his memories when he was born to Mark. The alien leader attacks the group, but Trent fights back inside a giant alien, and turn blue lights into red lights, defeating the alien leader. With Earth saved, Mark names the girl, Rose (after his deceased wife), who later grows up, as the red lighted aliens and humans launch their assault on the other blue lighted alien ships, including the mothership.