Transparent color slots are a programed and needed part of the Game palettes. Those transparent colors are used in the 256 color palettes and they are indexed. They are needed in this type palette for overlays. In other words, there are several images put together on the same screen. The Transparent color is used to allow this. Otherwise we would only see one image. The Buttons on the Title screen are one example. IF the background for those Buttons was not Transparent, their Background would Mask Out the Title Screen. There are many examples in the Game that show more than one image together with others. Each Image has a Transparent Background so when they are combined to show together on the screen, one does not Mask Out the Other. Units themselves use Transparent Backgrounds or we would see their backgrounds in the game while looking at the Game Map. In Units and other pcx files that have Frames, a transparent color is used to set the Frames Transparent. The Last two color slots are coded to be Transparent in order to Keep those Slots for transparencies. The colors in those slots are therefore discounted as actual available colors in the palette and will not be used as any of the colors in the palette that are applied to the images. The "programing" for the 256 Color Palettes remains the same and tells the computer what is Transparent. Then the Graphics Artists can use those slots to be able to combine multiple overlays on the same screen.