Sheeva was meant to play a larger role in the film, even to the point of early scripts having a two-on-one fight of her versus Liu Kang and Rayden. However, budget limitations meant it would be prohibitively expensive to have a long fight-scene involving her, due to the amount of prosthetics and CGI needed to portray the character's extra limbs; thusly her role was cut down to a few brief scenes and lines, and her fight-scene was hastily changed to her death-scene instead.
For years, a third Mortal Kombat movie was being developed by New Line Cinema to atone for the poor reception to "Mortal Kombat: Annihilation". mink was hired to direct, and then Russell Mulcahy was hired to replace him. Sean Catherine Derek and Lawrence Kasanoff took turns writing the script, which would have had Johnny Cage resurrected to help the heroes against Quan Chi and a resurrected Shang Tsung. However, according to cast member Chris Casamassa, who would have reprised his role as Scorpion, production was halted when Hurricane Katrina destroyed most of the sets and the film ultimately never happened.
Quan Chi was going to appear in the climax of Mortal Kombat: Annihilation, but his scenes were cut from the final print. He still appears in some posters and international versions of the movie on laserdisc and DVD.
Liu Kang's animality is to change into a dragon during the final kombat against Khan. Liu Kang changing into a dragon and biting off the top half of the opponent's body is one of his finishing moves in Mortal Kombat II (1993).
Ermac (the Red Ninja) is able to summon the shadow fighter Noob Saibot. According to the video game storyline, Ermac was created by Shao Kahn as an amalgamation of the souls of fallen warriors. (Which could explain how he summoned Noob Saibot) Ermac however, was one of the deadliest fighters in the MK universe; able to battle 5 strong warriors such as Johnny Cage, Kitana, Jax, Sonya Blade and Kung Lao all at once and reach a standstill. (If his characteristics on film had stayed true to the character's inception, his fight with Sonya would have been very brief.)
Robin Shou (Liu Kang) and Talisa Soto (Kitana) are the only actors from the first film to reprise their roles. The other main characters are portrayed by different actors. The only other actor to return was Keith Cooke, but as a different character. In the first film, he was Reptile. Here, he portrays Sub-Zero.
In the film, Jax fitted his arms with "muscle enhancers"; essentially a sort of exoskeleton that quadrupled his muscle capacity. However in the storyline for Mortal Kombat 3 (1995) (One of the shared premises for this film) Jax had his actual arms removed and fitted himself with the bionic arms.
In the initial Mortal Kombat storyline for the games, Noob Saibot is actually the original Sub-Zero and the popular titular character is the younger brother of the former. With the appearance of Noob in this film, keeping with the storyline would mean that he is in fact the same Sub-Zero that Liu Kang defeated in the first film.