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Mortal Kombat: Deception - Shujinko
Shujinko was a new character introduced for Deception's lengthy Konquest mode, and he was the focal point of that game's story. As a child, Shujinko was approached by a spirit that called itself Damishi and claimed to be an agent of the Elder Gods. This entity tasked Shujinko with gathering six relics known as Kamidogu, and they were spread throughout the realms (Earthrealm, Netherrealm, Chaosrealm, Outworld, Orderrealm, and Edenia). For decades, Shujinko learned the abilities of various kombatants in his quest to obtain all six Kamidogu. Upon completing his quest for the relics, he planned on presenting them to the Elder Gods. It was then that Damishi revealed himself as Onaga, who took the Kamidogu for himself. Shujinko retaliated by rallying many warriors, absorbing their abilities, and using his newfound powers to confront the Dragon King and shatter the Kamidogu. After Onaga was defeated, Nightwolf used his powers to bind the Dragon King's soul to the Netherrealm.
Mortal Kombat: Armageddon - Taven
This entry has faced much criticism from Mortal Kombat fans for its lackluster and confusing story (not to mention the lack of proper Fatalities). After spending a lot of time trying to find a clear answer to the "winner" of Armageddon, I understand why. Armageddon's big hook was that it featured every character that ever appeared in a Mortal Kombat game. In addition to this, it also introduced the new character Taven (along with his brother Daegon) as the protagonist of Konquest mode. After a long quest that involved facing his brother in Mortal Kombat, the Battle of Armageddon begins. This battle was predicted by the Elder Gods, and involved every kombatant in the series. The forces of good and the forces of evil fought in a gigantic skirmish, and a massive structure known as the Pyramid of Argus rose on the battlefield. Atop this pyramid was Blaze, who you might remember as being this guy (yes, that dude became the boss of a Mortal Kombat game). Whoever defeated Blaze would be granted their greatest wish, so all of the kombatants battled their way to the top of the pyramid to take their shot at the game's boss. Taven managed to kill Blaze, but an unexpected outcome occurred. This leads directly into the opening of...
Mortal Kombat (2011) - Raiden
After Taven defeated Blaze, all of the kombatants were blessed with increased powers. They all
wound up killing each other except for Taven, Shao Kahn, and Raiden.
Outworld's emperor and the Thunder God faced off, but Raiden was no match for Shao Kahn. Just before dying, Raiden sent a message back through time, to be received by his former self from the original game's timeline. At the beginning of this new timeline, Raiden's past self tries to understand the message of "he must win." He travels through an alternate version of the timelines from the first three games, trying to find the chosen kombatant that will save the world from Kahn. At the end, Raiden discovers that he's destined to win when the Elder Gods possess his body and assist him in defeating Shao Kahn once and for all (but not really).
Also, this was the title that rewrote the series timeline, and basically made it so none of the stuff I wrote about in this article ever happened.