The computer-controlled opponent AI was improved in the game. Combos that knock opponents in the air no longer send one's opponent to the level above in multi layered levels only regular uppercuts do this. Chain combos could be started by using a jump punch (vertical or angled) or a vertical jump kick, which creates more opportunities to use combos. Some characters were given extra combos and some combos were made to cause less damage. To balance the gameplay, some characters were given new moves and some existing moves were altered. Shang Tsung's transformations are accompanied by announcements of the name of the character he is changing into. Shao Kahn's Lost Treasures - selectable prizes, of which some are extra fights and others lead to various cutscenes or other things - are introduced after either the main game or the eight-player tournament are completed.

In the additional 'Master' difficulty setting, Endurance Matches return, in which the player can face as many as three opponents in a given round these had not been seen in the series since the first Mortal Kombat. The original red portal background used for the 'Choose Your Destiny' screen is now blue and an extra Master difficulty is present. Several miscellaneous features were added to and changed in UMK3. Two new gameplay modes were introduced: the 2-on-2 mode which was similar to an Endurance match but with human players on both sides, and a new eight-player Tournament mode.

Several ninja characters absent from Mortal Kombat 3 return in Ultimate Mortal Kombat 3, including Kitana, Jade, Reptile and Scorpion on the prototype version a new Ultimate Kombat Code was added in revision 1.0 to enable Mileena, Ermac, and Classic Sub-Zero as secret characters.

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