Like all of the Mortal Kombat games, Deadly Alliance focuses heavily on its fighting modes. The gameplay is completely different from that of previous entries in the franchise. Each character now possesses three individual fighting styles,[4] generally two hand-to-hand styles and one weapon style (except for Blaze and Mokap, who received three hand-to-hand styles and no weapon style) which players can switch between with the push of a button. In previous games, aside from "dial-a-combos" all the characters fought virtually identically, with only special moves to differentiate them. The number of special moves per character (usable in any fighting style) has also been reduced, varying only from two to four for most, thus forcing the player to make use of the improved fighting system. The characters can no longer run, and there is no run meter. However, while still limited to only moving into the background and foreground, movement in the third dimension is much easier and can be used continuously (in Mortal Kombat 4, sidestepping was mapped to two different buttons and could be performed at a rate of about one second). To prevent fighters from leaving the arena, boundaries that are otherwise invisible appear when a fighter is knocked against the edge.
Characters models became more realistic. Flesh will move or jiggle on a character as he or she moves around. Environmental interaction is present, but infrequent. Several levels include obstacles—such as pillars or statues—that can be shattered to damage an opponent standing near one. There is just one Fatality per character, while the previous games included many ways to finish the opponent. Along with Mortal Kombat X (until the XL patch added them to Mortal Kombat X), it is the only other Mortal Kombat game that does not include Stage Fatalities, although the Acid Bath level still possesses special acid-vomiting statues called Acid Buddhas that do damage directly to fighters that stray too close to them.