The character Rain (playable in some ports of the game) is a purple ninja palette swap. The co-creator of the game, Ed Boon, is said to be a longtime fan of the artist Prince; Rain's name and appearance is a reference to Prince's song Purple Rain.
In Mortal Kombat 3, due to the lack of traditional male ninjas in the game, the secret character Noob Saibot was a black palette swap of Kano, instead of being a palette swap of the ninjas as he was in Mortal Kombat II. In Ultimate Mortal Kombat 3, Noob was again brought back as a ninja palette swap. The Sega Saturn version, however, still contains the Kano Noob Saibot. This is because the Sega Saturn port of Ultimate Mortal Kombat 3 is actually a hacked version of Mortal Kombat 3 for the Playstation.
On August 31, 2000, Ultimate Mortal Kombat 3 was put on the infamous German index by the BPjS. For more information about what this means and to see a list of games sharing the same fate, take a look here: BPjS/BPjM indexed games.
In order to include as much as possible for the SNES port of the game, the character Sheeva (who was created using stop motion animation) was dropped to make room.