|Primary Location(s)||Black Water, Karda Nui (formerly), the Pit (formerly)|
Passing by Aqua Magna, the Great Spirit Mata Nui fell into a coma, and crash landed on the ocean planet. The waters of the ocean were affected by the natural energy radiating from the robot, and turned mutagenic. Large amounts of water containing Pit Mutagen leaked through the hole in the Southern Continent's dome, caused by Voya Nui breaking up through it, and into Karda Nui, where it created a swamp at the bottom. Prisoners attempting to escape from the Pit entered the waters, and were mutated. The Pit itself filled up with the mutagenic waters.
The landmass of Mahri Nui later broke off from Voya Nui, and fell into Aqua Magna. The Matoran there were affected by the Mutagen, but were saved by bubbles of air forming a protective dome around the city. The Mutagen had affected their bodies, but undid weakening alterations made to them by Karzahni. However, it also damaged some of their weapons.
In Karda Nui, numerous Rahi and three Makuta were mutated by the Pit Mutagen. The Makuta lost many of their powers and their ability to shapeshift, becoming locked in the insectoid forms they had taken for that mission, as well as being afflicted by a number of other mutations.
After Mata Nui reunited Spherus Magna, he sent a wave of Life energy throughout the planet, which, among other things, partially cured the mutated beings residing in the ocean of Aqua Magna, while leaving them able to breathe water.
In this alternate timeline, Pit Mutagen flooded into the domes of the destroyed Matoran Universe after Mata Nui's death, mutating any creatures that survived beyond recognition.
The Pit Mutagen is diluted from a form of energy radiation naturally emitted by energy sources, such as the Codrex. The energy itself is invisible, and is ordinarily harmless. However, combined with the Black Water of Aqua Magna, the energy formed a mutagenic substance. The mutagen alters the physiology of those affected, frequently rendering them unable to breathe air.
The Mutagen has mutated the Matoran of Mahri Nui and the Barraki, among other beings. The level of the mutagen's saturation in the waters of the Pit increases with depth; higher up, brief visits will produce no change at all, midway down exposure for a minute or so causes drastic changes, and near the bottom of the Pit complete mutation occurs almost instantaneously. Nocturn's species is immune to it, along with the Zyglak and Hydraxon. Pit Mutagen can also be damaging to Kanohi and weapons. Both the Ignika and Brutaka's Olmak have been damaged by it, as well as tools used by the Mahri Nui Matoran.
- The Barraki
- Keras Crabs
- The Matoran of Mahri Nui (Only reversed Karzahni's alterations)
- The Piraka
- Spinax (Amphibious)
- Swamp Stalker
- At least one Nui-Kopen
- Mistika Makuta
- The only known cures for the mutagen are the powers of the Kanohi Ignika and the power of the Great Spirit.
- The organic creatures of Aqua Magna are not immune to the mutagen; it simply affects them so slowly that the effects are almost unnoticeable.
- A quirk of Brutaka's species gives them a slight resistance to the effects of the mutagen; although it makes them water breathers just as quickly, it takes longer to change their physical appearance.
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