Mortal Kombat 3 builds further on the gameplay of the previous game. A "Run" button, accompanied by a "Run" meter, was introduced. This was primarily to address concern from fans who thought that the previous games gave too much of an advantage to the defending player. The Run meter is drained by running (the character cannot run backwards, only forwards) and by performing combos. "Chain combos", also known as pre-programmed combos (labelled "dial-a-combos") were also introduced. Chain combos are preprogrammed button presses that are unblockable once one hit connects (e.g., one of Sonya's chain combos is HK-HK-HP-HP-LP-b+HP). Some chain combos end with an uppercut or other move that knocks the opponent into the air, so that more punishment can be dealt via a traditional juggle combo. To please players of various skill levels, a "Choose Your Destiny" screen appears in 1-player mode. This new feature allowed player-selectable difficulty.
For the first time, certain levels were interactive by allowing characters to be uppercutted through the ceiling where both characters would continue the battle in a different stage. This could alter the game's level cycle. Both normal uppercuts and uppercuts that are part of a ground combo would result in a level change. Kung Lao's "Whirl Wind Spin" move would also have the same effect. However, if the final hit of a round happens to be an uppercut (i.e., the character is defeated by an uppercut), there is no level change.