Beating the Story will unlock some nice awards for you.
You will receive two trophies / achievements, called 'Back In Time...' and 'Quan-Tease'. Moreover Quan Chi will be added to your roster of playable fighters.

This final bossfight can turn out as a pretty annoying and time consuming event. Actually, you will need nothing but the teleport and uppercut attacks. Teleport yourself each time, Shao Kahn is taunting or shooting his spear / hammer on you. Try to keep the range between you an kahn as large as possible. He will more likely tend to perform one of his pointless taunt actions. When the luck is on your side, you will have no trouble getting this in your first couple tries.