Blake Stone: Aliens of Gold is divided into six missions ("episodes"). Each mission takes place in a certain location and follows the same structure - The player starts on floor 1 and must work their way to floor 9 to defeat the boss and complete the mission. Floor 0 (the "basement") is always a secret level that can only be accessed via a teleporter in another floor. Floor 10 is always a secret level that can only be accessed by finding a hidden access card in floor 9. Only the first mission is available in the shareware version.
There are a total of 66 playable floors. However, the actual number of floors in the game is greater; each mission contains hidden inaccessable floors. These floors are often very simple and contain few number of objects, although some have hidden messages in them; walls are arranged to form letters and words, viewable only with a map editor. The purpose of these extra unplayable floors is unknown, but most likely an easter egg. They can be viewed with MapEdit, a program that allows editing and creation of Blake Stone, Wolfenstein 3D, and Spear of Destiny levels.