Some elements from mortal kombat mk3 Advance are missing in this game.

Characters were given new moves and some existing moves were altered. The only biographies featured are those of Kitana, Jade, Scorpion and Reptile (the ninja characters who were not included in mk3),

which are the only four shown during attract mode, while all of the biographies and the full-body portraits of the mk3 characters are missing.

The game features several new backgrounds: Scorpion's Lair/Hell (this stage also contains a new Stage Fatality,

where an uppercut can send the opponent into a river of lava); Jade's Desert (in a reference to his mk3 ending, Cyrax is seen stuck waist-deep in sand in the background);

River kombat/The Waterfront; Kahn's Kave/The Cavern; Blue Portal/Lost (a combination of the background from the game "choose your destiny" screen, the Pit 3 bridge,

and the mountains and bridge from the Pit II in mortal kombat mk3 Advance); Noob's Dorfen (based on the Balcony stage,

which can now be played using a kombat Kode without having to fight Noob Saibot to see it as in game).

Before reaching any of the original backgrounds in 1- or 2-player mode, the game must cycle through all of the game exclusive backgrounds twice.

Scorpion's Lair, Secret Cave and Abandoned River stages are selectable by using a password while on the missing Bank Stage cycle.

In Scorpion's Lair, fighters can uppercut each other into Kahn's Kave.

The biographies that do appear in the game are presented differently from those in, as are the endings. The storyline images and text do not appear.

Finally, the Bank and Hidden Portal stages from mortal kombat mk3 Advance were removed (Jade's Desert serves as a placeholder where The Bank stage used to appear once the player reaches the original mk3 level cycle).