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At the end of the first timeline, Sora is first seen being defeated by Shao Kahn who has absorbed much power. In a last desperate act, Sora grabbed his Keyblade, and sent a message with visions ending it with "He must win!" before dying.
In the new timeline, Sora is met by Cao Cao at the Disney Castle and the teenage boy greets the Wei ruler as an ally. What the heroes did not know, is that Sora's girlfriend Kairi was already kidnapped and was being impersonated by Shang Tsung, who was leading Cao Cao on a quest for power. When a bomb nearly detonated under Cao Cao's bed, Sora began to suspect Kairi as the culprit for attempting to kill Shang Tsung. Later on, towards the end of the game, Sora is grief stricken when much of his friends fighting Lu Bu are killed. Cao Cao reminds the teen that he will go to Quan Chi for assistance, but Sora refuses, fearing Quan Chi will just turn on and kill him. Donald and Goofy inform Cao Cao that Sora had already gone to the vast lands of Outworld to rescue the pure hearts before the ritual. At the gates to Shao Kahn's fortress, Cao Cao tells Sora that defeating Shao Kahn before the ritual is complete will be temporary. After the fight between heroes, "Kairi" appears before them and Sora is at first relieved but then horrified when "she" kicks him to the ground. "Kairi" thanks Sora and Cao Cao for serving her well, but the shuriken of Hikage and the bullets from Rambo's machine gun save the heroes. With the unveiling of Shang Tsung as a distraction, Sora goes inside the fortress. The keyblade wielder arrives second in Shao Kahn's throne room as the ritual begins. Infuriated after Cao Cao again forbids him to stop the ritual, Sora lights his Keyblade on fire and prepares to kill the Wei ruler, but was mortally cut by an icy swing from Cao Cao's sword. The horrified Cao Cao begs for Sora to forgive him, and the last words from Sora before he dies was "Cao Cao... You... have killed... everyone..." At the end, he is revived by Tinker Bell's magic, then when he wakes up, he sees an alive Kairi smiling at him. Sora tearfully hugs his girlfriend and then forgives Cao Cao for his anger.
- (after seeing the visions in Cao Cao's amulet)The visions were from my future self?
- Cao Cao's response:Yes. "He must win." would be your last words before you die at Shao Kahn's hands. I have to choose the role of the victor carefully.
- Listen you Elder Gods! You have to help us! Innocents will die soon at the hands of Outworld! Thousands, no Trillions will be dead if Shao Kahn is igno-
- Male Elder God:We cannot help you. Shao Kahn has not violated the rules of Mortal Kombat.
- My friends... They're dead... The sacrifices were in vain! (Sora seeing his friends dead from the battle with Lu Bu)