Special Forces is chronologically the first game in the Mortal Kombat storyline, as its events take place even before Mortal Kombat Mythologies: Sub-Zero. Originally, the game was to expand upon the bitter relationship between Sonya Blade and Kano. The original demo shown in the 1996 E3 convention portrayed the first mission briefing, explaining it to be joint operation with a Eurasian Task Force in Hong Kong territory, to reclaim a nuclear warhead stolen by the Black Dragon, and under the guise of a drug sting. The demo included a scene where Kano captured Sonya and the first known apparition of Kabal before his mutilation in MK3. Unfortunately, the original plot was simplified after Tobias left the development team.

The final story of Special Forces portrays Major Jackson Briggs on a mission to stop Kano and four other Black Dragon members freed from a high-security prison (Tasia, Tremor, No-Face and Jarek) from reaching an artifact of great power, the Eye of Shitian. The true powers of the artifact are not revealed at all, although it is shown in the end that one power the artifact has is to open portals to other realms when Jax uses the artifact to teleport himself and Kano back to Earthrealm, once Kano is defeated.