From Glitch City Laboratories
This article is about the special case for a town map identifier of 00 "SPECIAL", for other uses such as the Special stat please see Bulbapedia's disambiguation page.
The term 'SPECIAL' appears for locations with an identifier of 0 on the Pokégear's Town Map section in Pokémon Gold, Pokémon Silver and Pokémon Crystal. In normal gameplay, although unnoticeable, it is used internally by the game as a special case for areas such as the second floor of a Pokémon Center (as this area actually exists as only one map location but is used throughout many towns and cities); the game will use this identifier to refer to the last location the player visited, and thus use that location as a basis for the new Pokégear map area that the player is in.
Another term, "Special Area" exists on Pokémon Ruby, Pokémon Sapphire and Pokémon Emerald and perhaps shares the same purpose, although since it is placed in between real locations with an identifier of C4 (196), it may instead, exist for a similar purpose to the many variations of Mystery Zones within the fourth generation handheld Pokémon games.
The term is also likely to have been left behind from Pokémon Red, Pokémon Blue and Pokémon Yellow as Pokémon Gold and Silver originally used the same engine, as was the case with the messages such as "You missed the Pokémon".