"There were few places darker than the outskirts of Mahri Nui. The only one Reysa could name was the watery region just below the city. The darkness there might as well have been a reflection of the hearts of its inhabitants."
— Narrator, City of the Lost
Beneath the former site of Mahri Nui
The Black Water is home to many dangerous marine creatures. It was largely unperturbed before the Great Cataclysm, which caused the structure of the Pit of the Matoran Universe to break open and release its inmates into the water. A large number of Rahi also migrated to the waters and integrated into the natural ecosystem. The entrance to the Pit was located here, as well as the caves of Barraki Pridak and Takadox, and the Razor Whale's Teeth rock formation, where the Barraki came to meet, after the Kanohi Ignika sank into the waters.
During the years following Mahri Nui's sinking, many Matoran vanished in the area and were never heard from again. For this reason, Defilak's Submarine crew was formed, composing of the Le-Matoran, a Ta-Matoran Sarda, a Ga-Matoran Idris, and an Onu-Matoran Gar, their mission being to explore the Black Water and hopefully discover the cause of the missing Matoran's disappearances. They were captured and taken into Pridak's cave for interrogation, although Sarda was tossed into the waters to waiting Takea sharks. The Ta-Matoran was rescued by Toa Lesovikk whose attack scattered the sharks. The two, while talking, were attacked by Karzahni. After being unable to defeat Lesovikk, the powerful being gave a horrific vision to Sarda, causing Lesovikk to break off the fight to save Sarda while Karzahni fled. Following Sarda's mutation into a water-breather, he and Lesovikk left to track down Karzahni. At around this time, the Ga-Matoran Kyrehx was kidnapped by the Barraki Carapar and taken to Takadox, who interrogated her about the Kanohi Ignika and, upon learning the mask was still in Mahri Nui, let her go.
Pridak later left his cave with Defilak to show him the scene of the Attack on Mahri Nui and tell him the tale of the Barraki. The other two Matoran escaped shortly after in the waters and made their way to Mahri Nui.
Takadox later came here to watch Mantax who regularly visited the Pit to search it. He was caught by Kalmah who demanded to know what he was doing. Takadox explained and hinted that Mantax might have hidden the Ignika in the Pit. The two then entered the Pit, only to be trapped in when Maxilos sealed the entrance. Nocturn arrived some time later and tore open the entrance, allowing the Barraki to escape while he challenged Zyglak in the Pit, who, due to Takadox's insinuations, he believed had insulted him.
Later, the traitorous member of the Order of Mata Nui, Brutaka, was dragged into the Black Water by a Giant Squid upon Pridak's orders. He was able to kill the squid, however, and began traveling through the ocean.
Upon obtaining the Ignika, the Barraki journeyed to the Razor Whale's Teeth where they left the mask in Nocturn's care, not trusting each other with it. Nocturn later grew bored with guarding it and, discovering his curse by the Ignika, left the Black Water to inform Ehlek. Toa Mahri Matoro was later brought into the Black Water by Hydraxon's replica, to be imprisoned in the Pit, as the jailor was recapturing all prisoners and believed that anyone in the ocean was an escaped prisoner. He was freed by a Maxilos robot which was possessed by the Antidermis of Makuta Teridax, and left the region with him. The two later returned and entered the Pit to find the corpse of an alternate Toa Mangai Tuyet which Matoro reanimated on the Makuta's order. The three then left the area again, to meet with Makuta Icarax.
Later, after Mantax acquired the Ignika, he called a meeting at the Razor Whale's Teeth, in which he revealed the Tablet of Transit he had discovered in the Pit and its significance in revealing the presence of a traitor among the Barraki. After the meeting was disrupted by an avalanche caused by Hydraxon, Takadox, the traitor, attempted to use the confusion to his advantage, although he was subsequently paralyzed by Mantax's venom and was also unsuccessful in his attempt to hypnotize the Maxilos robot possessed by Teridax, into attacking the other Barraki.
After the Pit's structure was repaired by the Staff of Artakha, Hydraxon, with the help of Lesovikk and Sarda, was able to capture several prisoners, including the Barraki, and bring them back into the jails.
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