In most versions of the game, there's a way to fight a secret character called Reptile. Deciphering the clues that are given in between random matches will lead the player to finish a fight on The Pit stage with two perfect rounds, without blocking, and when shadows pass over the moon. If this is done, the next round will be with Reptile, who has a combination of Sub-Zero and Scorpion's move sets, as well as displaying Scorpion's name.

According to Guinness World Records, Reptile is certified as the first ever secret character in a fighting game.