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After Earthrealm won the tenth tournament, Tarkatans invaded Earthrealm. The defenders killed all the Tarkatans, but Baraka and Shang Tsung managed to escape- and kidnap Sonya Blade. Shao Kahn starts the new tournament by having Jax verse Baraka. Jax won and then he, Johnny Cage, and Raiden went into the armory where Jax defeated Jade, and were then led to the acid pools. In the meantime, Liu Kang and Kung Lao were sent to free their Shaolin ancestors. In the acid pools, Sheeva and other Shokan were holding Sonya captive. They were defeated and, on her wrist COM, Sonya picks up two transponders from Earthrealm. Those two transponders end up being Earthrealm ninjas called Smoke and Tundra. They are after the person who killed Tundra's brother, Sub Zero. They split up, Smoke goes in the forest and Tundra goes into a large building. Smoke ends up defeating Reptile, Kitana, Kano, and Shang Tsung as Sub Zero. He also encounters Cyber Sektor. Tundra defeats Ermac and Cyber Cyrax. He then gets led to the colluseum where he defeats Reptile. He then avenges Sub Zero's death by defeating Scorpion. Tundra then gets captured by the Lin Kuea cyborgs. Kitana is then blamed for their defeats for allowing Smoke and Tundra to get there. She then meets up with Raiden, where she battles Smoke and Johnny Cage. She then is told to go to the fleshpits, where, on the way, she defeats Jade. She then reaches the fleshpits where she discovers replicas of her mixed with Tarkatan blood. She then battles one and defeats her, as well as Shang Tsung. When she reaches Shao Kahn, she discovers that Shao is not her real father. She is then captured by Sheeva. Jade then realizes that she has to rescue Kitana. She defeats Smoke in a misunderstanding, Baraka, Sheeva, and the creature Kitana fought in the fleshpits, now called Mileena. Kitana tells Jade to leave, and Kitana then gets taken to the colluseum. Kung Lao and Liu Kang then go to the tower where they battle Sheeva, Goro, and Noob Saibot. Goro informs them of Kitana's execution. At the colluseum, Kung Lao defeats Shang Tsung, Quan Chi, and Kintaro. He is then killed by Shao Kahn. This enrages LiubKang who ends up battling, defeating and killing Shao Kahn.

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