Mutagen

The mutagen was a type of energy present in the Pit's waters which mutated almost any being exposed to it into a water-breather that resembled a sea Rahi. The mutation only took minutes of exposure to take its effect, and it was impossible to reverse without the Mask of Life.

It has been confirmed (via Greg Farshtey and BZPower) that Mutagen was never intended to mutate beings. It was originally designed as a form of power source, much like nuclear energy in our universe. It was used to power the Dome Islands (Metru Nui, Karda Nui etc.). The mutagen was contained in two 'reactors' - one on Karda Nui, one on Metru Nui, which powered the lightstones around these Domes. During the Great Cataclysm, power lines carrying the energy (one of them just beneath the Pit) cracked, releasing Mutagen into the surrounding areas.

Known Beings Mutated

 * Barraki
 * Pridak
 * Kalmah
 * Ehlek
 * Takadox
 * Mantax
 * Carapar
 * Sarda
 * Idris
 * Matoran of Mahri Nui (reversed damaged done to them by Karzahni)
 * Brutaka (Breathing Apparatus)
 * Lesovikk
 * Spinax (slightly)
 * Karzahni
 * Piraka
 * Zaktan
 * Hakann
 * Vezok
 * Reidak
 * Thok
 * Avak
 * Most of the Pit's prisoners
 * Keras
 * Makuta Bitil, Gorast and Krika
 * Niazesk
 * Nui-Kopen

Known Beings Immune to the Mutagen

 * Hydraxon
 * Brutaka (slightly)
 * Zyglak
 * Hydruka
 * Organic Rahi
 * Nocturn
 * Toa Inika\Toa Mahri

Trivia

 * The Kanohi Ignika was being dissolved by the Pit's waters during the 2007 storyline, and as it did so it let off small amounts of its power.
 * On the way to the Chamber of Life, there was a large pool of water that the Piraka fell in that contained the mutagen.
 * Greg Farshtey has revealed that the mutagen was caused by the Great Cataclysm.
 * Botar has not been changed by the mutagenic waters of the Pit because he has never stayed long enough to be affected (he deposits his prisoners and leaves within a fraction of a second before he can even get wet) - in fact, he has not even noticed that the Pit has been flooded.
 * In most cases, a side-affect to exposure was being mutated into a sea rahi-like form.
 * The Toa Mahri were not changed into water-breathers by the Mutagen, but by the flash of energy the Ignika emitted as a cry for help.