List of deleted Skulls
From Halopedia, the Halo wiki
This is a list of Skulls cut during the development of Halo games.
Halo: Combat Evolved
In the level Keyes, the Master Chief originally had to burn through the Proto-Gravemind's biomass to retrieve Captain Keyes' neural implants. Bungie modeled a burnt skull, which was said to be particularly gruesome. The scene and Keyes' skull were cut due to the flamethrower being deleted from the game.
The unknown skull in the level Cortana was originally designed to be the Blind Skull ("Interred deep within her tomb"), whereas the first skull in the level Sierra 117 was originally the Assassin Skull ("Interred where heroes fall"). Bungie eventually swapped them, putting the Blind Skull in Sierra 117 and leaving a nonfunctioning Assassin Skull in Cortana. The latter can still unlock the Blind Skull and, if carried throughout Cortana, will make the player start with a Spartan Laser as a primary weapon at the beginning of Halo. The names and descriptions of these two Skulls can be found in the game's files. In the final game, the Assassin Skull is the only skull that does not appear in the Skulls menu.
Halo 3: ODST
The skull was supposed to shift the player's view to third-person, much like in Theater.
The skull was supposed to activate developer commentary while the player went through the game.
Halo: Combat Evolved Anniversary
Weapon sound effects
According to a 343 Sparkast, the skull was supposed to replace weapon sound effects by 343 Industries staff saying the noise, such as "bang".