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 (labeled "dial-a-combos") were also introduced. Chain combos are button sequences that cannot be interrupted once one hit connects; some chain combos end with an uppercut or other move that knocks the opponent into the air, so that more damage can be dealt via a traditional juggle combo. To please players of various skill levels, a "Choose Your Destiny" screen appears in the single player mode to allow player-selectable difficulty.
For the first time, certain levels were interactive by allowing characters to uppercut each other 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 character is defeated by an uppercut, there is no level change.
All of the different styles of finishing moves featured in Mortal Kombat II (Fatalities, including the non-lethal Babality and Friendship moves) return in MK3. Additionally, the rumored Animality, where the character transforms into an animal in order to kill their opponent, is featured for the first time. Another new addition is the Mercy, where the character can give their opponent a small sliver of life if they have won two rounds and are at the "Finish Him/Her" screen. A Mercy is necessary for an Animality to occur. Finally, three new Stage Fatalities can be performed in the Subway, the Bell Tower and the Pit 3.
Another concept introduced in this game is the "Kombat Kode". A Kombat Kode is a six-symbol code entered at the VS screen in a two-player game to modify gameplay, fight hidden characters or display certain text messages. Also introduced in this game was the "Ultimate Kombat Kode", a 10-character code using symbols, that could be entered on the game over screen after the continue screen disappears in single player mode. It was used to unlock a robotic version of the character Smoke; it can be done by either the player or the arcade operator. The arcade owner could reset this code by accessing the game's diagnostic menu by toggling a DIP switch within the MK3 cabinet. The codes were revealed through gaming magazines, promotional material and other Mortal Kombat media.