Jax was hot on the trail of Black Dragon criminal Kano, when he was led into the Mortal Kombat tournament. Kano represented the criminal underworld and Mortal Kombat was the supernatural event that caused all of these things to collide. But, they only hinted at their shaded past.  Lt. Sonya Blade and Kano disappear after the first tournament. Jax takes a risky rescue mission to the Outworld. He must save his partner Sonya and stop Kano once for all.

Of all the Mortal Kombat games, this game is considered to be the worst. This has much to do with the fact that many of Midway's staff, including series co-creator John Tobias, had left the company for various reasons. Tobias eventually founded Studio Gigante, the creators of the Mortal Kombat imitation Tao Feng: Fist of the Lotus.

This was the second Mortal Kombat game that wasn't a fighting game, the first being Mortal Kombat Mythologies: Sub-Zero. Tobias intended to work on a series of non-fighting games to expand the Mortal Kombat universe, including games based on Baraka and the Shaolin Monks Liu Kang and Kung Lao, the latter of which was actually released recently by Midway.

Mortal Kombat: Special Forces sold so terribly that Midway placed the series on a hiatus in preparation for Mortal Kombat: Deadly Alliance . It was the last Mortal Kombat game to be released until the release of Deadly Alliance in 2002.

Sonya was originally supposed to be playable. Due to Midway cutting a lot of things after Tobias left, she was left out. Instead, she appeared to be Kano's prisoner.