After the events of Red Alert 2 the leadership of the doomed Soviet Union devises a plan to travel back in time and assassinate Albert Einstein (whose own time travels led to the events of the previous two games) in order to change history and restore the Soviet Union as a world power. However, during the mission, something goes quickly and horribly wrong and an "alternate timeline" is inadvertently created, erasing the events of the previous two games, which alters the technological evolution and creates a new, technologically advanced superpower in the East, known as the Empire of the Rising Sun (i.e. Japan). And thus, a World War breaks out among the Soviets, the Allies and the Empire and is fought with exotic weaponry such as "Tesla coils, heavily armed War Blimps, teleportation, armored bears, intelligent dolphins, floating island fortresses, and transforming tanks".
All information from wikipedia