Same story, more fighters.
The story for UMK3 is that same as its predecessor. Shao Kahn invades Earth and Outworld merges with it.
The controls remain the same with simple punches and kicks, plus the run button.
Graphics haven't changed either.
Unlockables and secrets include the ability to use Shao Kahn and Motaro as playable characters. Human Smoke is also playable by choosing the cyborg version and holding down a certain order of buttons. The console versions allow Rain and Noob-Saibot to be playable unlike the arcade version. Ermac, Classic Sub-Zero, and Milenna don't have to be unlocked by a code as well.
Midway was right to make this update. It made the fans happy and the game still is being ported to this day.