Command & Conquer: Red Alert 3 is set in an alternate reality from World War II, in which the Western Allies fought the Soviet Union. In Red Alert 3 the Soviet leadership, facing defeat, goes back in time to kill Albert Einstein and prevent his assistance to the allies, paving the way for Soviet domination in the present. However, as an unintended consequence, a third world power, the Empire of the Rising Sun, is created and all three sides go to war.

On the brink of defeat at the hands of the Allied Nations, the leaders of the Soviet Union make a desperate gamble. Using a time machine hidden beneath the Kremlin, Colonel Anatoly Cherdenko and General Nikolai Krukov travel back to 1927 to assassinate Albert Einstein, hoping to erase the technologies that doomed them and rewrite history in their favor. When they return to the present, the world has indeed changed: the Soviets stand poised to conquer Europe, but without Einstein, nuclear weapons were never invented. Into this altered timeline storms a new power, the Empire of the Rising Sun, which declares war on both the Soviets and the Allies in pursuit of total domination. The meddling with time has ignited a fresh Third World War, now a three-way struggle between the Soviet Union, the Allies, and the Empire.