Board Thread:Mortal Kombat X/@comment-1084762-20140624043237/@comment-12973094-20150315080804

My guess for the surprising final boss:

Shujinko!

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He was at the back stage of every edition, meeting characters all over, and harnessing thier powers.

If somebody changes one event on the timeline, everything mutates. Now, an evil Shujinko is very plausible, since Onaga was manipulating him. Shang Tsung is dead, so, no Deadly Alliance; Shao Kahn is dead or imprisoned by the Elder Gods, so, Outworld is in the hands of another ruler, Kotal Kahn or Mileena; Shujinko has an entire new story to follow since the last timeline was rewritten.