Select Ultimate Mortal Kombat 3 from the main menu and fight your way up the ladder until you've defeated all kombatants. Shao Khan is the final boss.
The Sub-Zero method works again here. Just freeze your opponent in place () then uppercut repeatedly. This does NOT work on Jade however as she can become invincible through projectiles.
Most of the cast can also be defeated easily with Sektor. Jump into them and then in the air, input his move to do the teleport uppercut. You'll usually hit them as they won't be blocking (because you jumped) and you can kick them on the way down (time it right).
Motaro: Probably the easiest of all the bosses across the games, it doesn't matter who you go here as special moves are mostly useless and too slow. Here's how I did it: Jump back from him and he will jump towards you. As his jump is so slow and awkward, you can quickly jump forward and kick him in the face. Then repeat jumping back and jumping forward to catch him off guard. He is VERY vulnerable in the air. Don't get too close though as his grab has great reach.
Shao Khan: Sub-Zero freeze method again works a treat. Make sure you freeze Shao Khan just as gets up. He's so big that you'll be able to uppercut him from his half stance.