Like all other Command & Conquer real-time strategy games, up until the expansion pack of Tiberian Sun, Firestorm, Command & Conquer: Red Alert 2 contains two distinct story lines depending on which faction the player wishes to play as. Both of the story lines differ in several distinct ways. However, the Allied story line is canon due to the way in which the expansion pack continues.

After the attempted conquest of Europe, the Soviet Union is in utter ruin. Joseph Stalin is dead, and the Soviet military has been all but destroyed. The Allies determine that a regime change would cause mass unrest in the Soviet Union, and in order to gain both support and stability in the region, the victorious Allies name Alexander Romanov, a distant relative of Czar Nicholas II, as the puppet Soviet Premier. Romanov acquiesces to the Allies' demands at first, though he builds up the Soviet military for "defense purposes" – a cover for an intended invasion of the United States of America.

The game's story line starts off with the American military being caught completely off guard by the sudden massive Soviet invasion of the USA, with Soviet aircraft, naval vessels, amphibian forces, and paratroopers coming in on both the East Coast and West Coast and with the majority of Soviet ground forces coming in through Mexico, which had recently voted in a communist government. The USA attempts to retaliate with the use of nuclear missiles, but Yuri, leader of the Soviet Psychic Corps and Premier Romanov's top advisor, uses his mind control to manipulate the personnel charged with launching the warheads and leaves them to explode in their silos. Within hours, the USA is overrun with Red Army troops. In the introduction video, Kirov Airships can be seen entering San Francisco, while large amounts of Soviet Conscripts are paratrooped down. Apocalypse tanks, Rhino tanks and V3 Rocket trucks enters the shoreside from the sea, while Soviet Dreadnoughts are seen launching their rockets simulateously at the Statue of Liberty and the surrounding area. In response, the US President Michael Dugan establishes an emergency response team headed by General Carville and the Commander known as "The Ghost" (the player) to the Soviet army later in the game.