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Most of the music in this game is comprised of multiple source audio files playing at once, to give it a self-composing feel.

The number of puzzles solved in the current age determines which set of music files plays. If none or all four of the puzzles are solved, then the files are drawn from the resource folder LI_T, EN_T, or MA_T, where LI stands for Edanna (life), EN stands for Voltaic (energy), and MA stands for Amateria (matter).

Otherwise, the music is drawn from the folder LI_M, EN_M, or MA_M. Each file within these folders has a 1, 2, or 3 in the filename to specify exactly how many puzzles must be solved in that age for that file to play.

Here's how the music is "composed". Usually, a file denoted as the "pad" loops indefinitely (though in some cases two different pad files are used). On top of that plays a sequence of "mldy" files, usually timed to harmonize with the pad (sometimes another label such as "pipe" is used). Various effects such as "stinger", "bells", "drum", and "squeal" chime in randomly throughout. Some examples of filenames are LI_THEME_pad2.wav, EN_M3_noise4.wav, and MA_M2_mldy5.mp3.

Many of the tracks in the Official Soundtrack are special arrangements and embellishments of the compositions within in game, particularly those found in the M folders. Therefore, these tracks are not actually present within the game, at least not in their exact form.