The Nintendo 64 version, due to limitations of cartridge space, lacks the classic versions of Raiden, Kano, Jax, and Kung Lao, and as well as Goro and Kintaro. Basically, Chameleon is a newer version of MK1 Reptile, but Chameleon randomly changes his color, not just his stance. In order to play as him, you have to perform a special button combination before the battle starts. This character, known as Chameleon, appears and rapidly switches between all the male ninjas ( Classic Sub-Zero, Scorpion, Reptile, Ermac, Rain, Human Smoke and Noob Saibot). Bosses Goro, Kintaro, Shao Kahn, and Motaro are also now playable. Along with the Ultimate Mortal Kombat 3 roster, Mortal Kombat Trilogy adds Baraka, Johnny Cage, Raiden, and 'klassic' versions of Raiden, Kano, Jax, and Kung Lao. Rain and Noob Saibot are playable for the first time with their very own moves, combos, and finishing moves.
Every character that has ever appeared in a Mortal Kombat game prior to Mortal Kombat Trilogy appears in this game.