Red XIII had a subplot that was cut from the game as the plot developed in a different direction. Originally there were to be two Red XIII clones created by Hojo called Cobalt XIV and Indigo XV. The player would have to fight all three of the "Red XIIIs" and figure out which was the real one, with the three swapping places periodically. Defeating the real Red XIII by accident meant the player had to fight the following boss battle with Hojo with only two party members. Cobalt and Indigo would return in the final dungeon of the game, turned into cyborgs and determined to prove they were superior to the real Red XIII.

There is a hidden "Red Man" in the Corel Prison. The model is hidden from view in normal gameplay. There are no other models like this in the game, and it is thought to be a signature from one of the designers.