This was due to avoid having to re-animate the fatality for this game. Sub-Zero's famous 'Spine Rip' Fatality reappears in the game but is completely censored, as the screen blacks out with only the 'Fatality' text visible. Additionally, Shao Kahn gained a throw and grab-and-punch move, and Motaro gained a proper throw move. These special moves included MK1 Kano's Knife Spin move, MKII Kung Lao's Air Torpedo, Goro's Spinning Punch move, Raiden's Lightning that shoots from behind the opponent, and Baraka's Blade Spin move.

Some were simple edits of existing moves (such as Stryker throwing two grenades instead of one), while others were unused animations never implemented in their intended previous games.

Many characters gained additional special moves. Once the bar is filled, it grants the character fast movement and greater attack damage for a short period of time. Mortal Kombat Trilogy introduces the 'Aggressor' bar, which fills as the combatants fight (twice as much if the opponent is blocking). The HUD is the same as from MK3/ UMK3, while the Aggressor bar is exclusive to MKT. Further information: Gameplay of Ultimate Mortal Kombat 3 Raiden from MKI battles the MKT version of Johnny Cage in MKII's armory stage.