The core gameplay objective of each mission is focused on gathering resources for building new units and structures, and then utilizing all available military forces to make real-time decisions in offensive, defensive and tactical moves that can surprise the opponent. Similar to the other games set in the C&C franchise, the presentation of the game uses not only the in-game assets to tell the story in cinematics, but also real-life actors that are filmed on stage. Red Alert 3 thus features three large campaigns focused on Western Allies (which are focused on high technology and strong units), Soviet Union (which promotes the use of large amounts of weaker units), and Empire of the Rising Sun (which features transformable units), all featuring wide array of hand-made missions, cooperative play and unique units, structures and gameplay tactics. However, the unexpected consequence of this historical change leads to the rise of the Empire of the Rising Sun, which serves as the third controllable faction.

During the events of this game, the almost defeated Soviets managed to turn the tables of the conflict by time-traveling again to the past and killing Albert Einstein, thus changing the history enough to give them the chance to fight back against Western Allies.

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