The story picks up right where Red Alert 2's canonical Allied ending left off. While the Allies focused on reclaiming territory and mopping up forces loyal to the deposed Soviet Premier Romanov, Romanov's advisor Yuri secretly raised an army of his own, drawing on his mastery of psionics and genetic mutation. When Yuri reveals himself, a global network of "psychic dominators" comes online in a bid to enslave the entire world. American President Dugan orders an air strike on one such device on Alcatraz, and though the attack fails, a crashed Harrier damages its power supply. As the rest of the dominators activate, the Allies scramble to power a time machine to undo it all — and at this point, the player chooses to side with the Allies, or to join the Soviets and steal the time machine to defeat Yuri while restoring the Soviet Union to power. Notably, Yuri's own army receives no single-player campaign — the first and only time in the series that a playable faction has gone without one.