(read my "character list" for appearences of characters.

quan chi wants to rule outworld and earth realm but he can't do it alone. Quan chi wants to find someone who is willing to do the job and someone he should be able to kill when he no longer needs them so that he can rule alone. This person happens to be shang tsung. he uses his amulet to resurect him but in the process shinnok escapes as well and he in turn resurects khan. Quan chi fears the alliance of khan and shinnok and doubts shang tsungs abillity to handle the threat, so he gets warriors(not yet confirmed which warriors are at quan chi's aid an which ones are on shinnok's) but quan chi for sure qets cyrax.
shang tsung tell cyrax to go on a suicide mission. cyrax crosses pathes with kung lao who was on his way to warn liu kang of the deadly alliance. cyrax looses and runs so that he can fulfill the mission. he enters the palace with stealth tech. and kills shinnok with what appears to be a mini atom bomb from movie pics. with shinnok dead. quan chi and shang tsung are on there way to kill shao khan.
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(fights and main storyline fillers happen durring this part of the timeline)

Quan chi kills shao khan and then finishes off shang stung before he could suck the emperor's soul so now quan chi has shang tsungs soul(and yes quan chi sucks souls)and the emperors(with all this power it gives the film the feeling that it is the hardest fight yet for liu). Suby who is now a main character teams up with liu and raiden to defeat the soul charged quan chi dies a large energy blast(oh yeah when shang tsung dies quan chi uses the amulet to use the abandond soulnado that shang tsung had nicely given him the location of)causes that realm to crumble. the others use raidens portal to escape but liu kang stays behind to free his brothers soul(must be done by ripping the amulet from his chest and liu kang dies the end.