With the addition of a second screen, the actual fighting between the characters and the puzzle gameplay itself are on separate screens so as to no longer obscure actions being made or planned.

Included is the return of Puzzle Kombat from Mortal Kombat: Deception, though the locked characters have to be unlocked by accomplishing specific feats during gameplay, as there is an absence of a Krypt.

With the addition of a second screen, players can now view the movelist and finishers of whatever character they are playing as during gameplay, though range specifications and Stage Fatalities are not displayed. Players must touch the slots in the allotted time a specific number of times based on the original Kodes to unlock them. The Ultimate Kombat Kodes have been cut in half, resulting in five slots due to only one player input. However, once unlocked, they remain so even after the game is turned off. The character roster is exact the same one as the arcade version with Classic Sub-Zero, Mileena and Ermac being locked from the start. It is notable for being a near-perfect port of the arcade version. Ultimate Mortal Kombat is a handheld port of Ultimate Mortal Kombat 3 released for the Nintendo DS.

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