Mutagen, also called Ooze, is a mucilaginous substance that has the effect of causing any creature exposed to it to increase in size, strength, and sometimes in intelligence. It is responsible for mutating many of the characters in the series, particularly the four Ninja Turtles.
In the Turtles of Grayskull series, Krang had been supplying Skeletor with mutagen in exchange for his dark magic. The Turtles burst into the TCRI building and interrupt the evil party, causing an explosion that opens a paradimensional tear. This pulls the Turtles, Krang, Shredder and many Foot Clan flunkies to the planet Eternia. Once there, the Turtles learn that combining the mutagen with dark magic creates a new purple colored ooze that turns any henchman into, as Michelangelo says, a total boss.
Near Snake Mountain, Skeletor sets up a mutagen production quarry which features an Ooze Pit. Skeletor, Krang and Shredder utilize the Ooze Pit to transform henchmen under their control into mutated creatures more powerful than before. The Ooze Pit is also used to transform captured heroes, which places them under the control of their evil masters.