Mortal Kombat Trilogy introduces the Aggressor bar, which fills as the combatants fight (twice as much if the opponent is blocking). When the bar fills, the character becomes much faster and stronger for a short period of time.

A finishing move known as a Brutality is featured in this game: it requires the player to perform an 11-button combo which causes their opponent to explode. (Brutalities were also added to the Genesis and SNES ports of UMK3.) All of the levels that featured a Stage Fatality made it into this game except for the one in The Pit II. Because of the practical impossibility of filming new, extra animations with actors for the non-Mortal Kombat II character sprites for the Pit II's overhead fall, they simply left the Fatality out entirely.

Many of the characters have brand new special moves and finishing moves. Several have unused special moves never implemented in previous games which made their first official appearance in Mortal Kombat Trilogy. These special moves include MK1 Kano's Spinning Blade 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. In addition, Shao Kahn has a throw move and a grab and punch move that is exclusive to this game, and Motaro has added an overhead toss to his arsenal.

Almost every battle arena that has been featured in MKII, MK3, and UMK3 makes an appearance in MKT, however only a handful of backgrounds from the first Mortal Kombat make it into this game (Courtyard, Goro's Lair, The Pit, and The Pit Bottom). The PC, PlayStation, and Saturn] versions only lack The Hidden Portal and Noob Saibot's Dorfen from MK3, while the Nintendo 64 version lacks Kahn's Arena and The Bank from MK2 and MK3, respectively. In some of the Kombat Zones a character can be uppercutted into different backgrounds: The Subway → The Street, The Bank → The Rooftop (only in the PC, PS and Saturn versions), The Soul Chamber → The Balcony, Scorpion's Lair → Kahn's Kave, Goro's Lair → The Armory → Kombat Tomb (N64 exclusive).