Scales was used as a puppet by Andross throughout the game. Andross made him more powerful in order to defeat the EarthWalkers, and he removed the SpellStones, which led to Sauria breaking apart. He led the SharpClaw army to war against the Cloud Runner tribe on the planet of Sauria and was the one responsible for the break up of the planet by removing the Spellstones that stabilized the planet and thus conquering each floating land mass one after another while using CloudRunner Fortress as his base of operations. However, Fox managed to stop him at every turn.
Later revealed to be the holder of the last of the Krazoa Spirits, General Scales prepared himself to fight Fox McCloud in the Krazoa Palace. However, this was not to be, as the spirit of Andross interrupted their fight and forced Scales to relinquish the final spirit to Fox.
As the general falls, he states "You will regret this," implying that he would return in a future title. However, since he is nowhere to be found, it is assumed that he has died. The only other explanation for his statement would be that he may have been warning Fox of Andross' return. However, because Scales did not know of his association with Andross, let alone could see Andross, this is highly unlikely.
When Fox returns from fighting Andross, he finds that the SharpClaw have liberated themselves from the general and are holding up his belt in victory.