The events of Armageddon has just ended and Shao Kahn has beaten Raiden. But just before Raiden could be finished he sent a message through his mind to his younger self during the first Mortal Kombat tournament. He sent it to warn him about the future but the younger Raiden doesn't understand the message. So the events of the the first three tournaments will be altered in the perception of Raiden trying to change the future.