The game takes place in 2058 in the Italian Red Zone, where GDI RAID troops under the command of Ricardo Vega battle Scrin forces of a second invasion force. Characters from the novel appear in the game, including Tera Gallagher.
The first mission is a recon into the vicinity of Threshold 19, where Vega and his squad, aided by a Nod priestess, Maja, are to investigate reports of anomalous activity. At the end of the mission, Scrin invasion force arrives, setting the story for the rest of the game.