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- "If you are truly about to face great trouble-danger on behalf of Mahri Nui ... we would be honored to call you Toa Mahri."
- ―Defilak, Prisoners of the Pit [src]
After the events on Voya Nui, Axonn opened a secret passage for the Toa Inika to descend through, known as "The Cord". When journeying down the cord, the Toa Inika fought against the Zyglak, and in the midst of the battle, a 300 Feet Mutant Venom Eel made cracks in the cord while squeezing it. The Inika exited through a crack and into the cold waters of The Pit, where they transformed into their current forms, due to a large explosion of light from the Ignika, giving them new Kanohi masks and Toa Tools. They later fought the Mutant Venom Eel, which was defeated by Hewkii using his Kanohi to send the eel crashing down to the seafloor.
After being transformed, the Toa spotted the underwater city of Mahri Nui where they encountered the Matoran there. At first, the Matoran of Mahri Nui were skeptical of these Toa, and refused to let them into their underwater city. In order to gain their trust, the Toa split up. Matoro was to stay with Defilak to negotiate, and the rest were sent to defeat some 5000 Keras crabs in the Fields of Airweed. When the Barraki, Carapar, withdrew his army, Idris reported to Defilak that the Toa Mahri looked like partners to the Barraki. Matoro tried to make a break for it, freezing the water around them to escape. However, he was quickly captured and held by Hydraxon. However, the robotic guardian Maxilos, with Makuta Teridax controlling it, freed the Toa. Matoro then followed the Makuta into the ruin of the inner Pit, where he was forced to revive the corpse of Toa Tuyet. While traveling to a meeting place with Makuta Icarax, the pair was attacked by Karzahni. After a swift battle, Teridax emerged victorious, and Karzahni left even more insane than before. Shortly afterwards, Icarax gave the Staff of Artakha to Teridax, who had plans of recreating the Nui Stone with it. However, Brutaka intervened and provoked a fight, during which he had Matoro flee.
Meanwhile at the Fields of Airweed, the other Toa Mahri were captured by the Barraki. The Barraki placed each Toa into caves and stationed Rahi from their armies to guard them. Here, Hewkii and Nuparu discovered an artillery room of the Barraki's and stole the Cordak Blasters from it. The pair ran into the rest of the group and gave them each a Cordak Blaster, and Kongu decided the replace his melee weapon with a second blaster. After some discussion, each Toa was given a task to perform, and they separated again.
After Mantax obtained the Ignika, the team reunited. Hahli proved they were on the Matoran's side, and Defilak, now convinced that the Toa Mahri were going to fight the Barraki, named them "Toa Mahri." Matoro later informed the Toa that in order to save Mata Nui's life, they have to destroy the Cord to send Voya Nui back to it's former position, but it would destroy Mahri Nui on the way. So the Toa had the Matoran evacuate their city, and then took them to the caves under Voya Nui for protection. On their way there, the Toa were ambushed by the mutated Piraka, who threatened to kill all of the Matoran if the Toa did not surrender. Suddenly, both the Toa and Piraka were knocked unconscious by a mysterious blast of power.
After they awoke, the Toa learned that the blast came from Axonn, who later led them to a cave that contained the Toa Terrain Crawler. They used the Rahi to quickly go down The Cord. After a ferocious battle with the Barraki and Hydraxon, the Toa destroyed The Cord with their Cordak Blasters. The Toa Mahri obtained the Kanohi Ignika, just as the Great Spirit Mata Nui died. Matoro decided to use the Kanohi to bring back Mata Nui while the others risked their lives to try and buy Matoro time. Matoro managed to get into the universe core, Karda Nui, before Voya Nui covered the hole to Karda Nui, and then he used the Ignika, killing himself in the process. However, during his last moments as an individual, he teleported the other Toa Mahri back to Metru Nui, where they became amphibious by the power of Matoro and the Ignika. They later returned to protect Metru Nui, until they came under the control of a golden-skinned being.
The Toa Mahri include:
|Jaller, (Leader) Toa of Fire||Arthron, the Great Mask of Sonar||Power Sword, Cordak Blaster|
|Hahli, Toa of Water||Faxon, the Great Mask of Kindred||Protosteel Talons, Cordak Blaster|
|Kongu, Toa of Air||Zatth, the Great Mask of Summoning||Two Cordak Blasters, a melee weapon (formerly)|
|Hewkii, Toa of Stone||Garai, the Great Mask of Gravity||Aqua Warblade, Electrified Chain, Cordak Blaster|
|Nuparu, Toa of Earth||Volitak, the Great Mask of Stealth||Razor-Edged Protosteel Shield, Aqua Blaster Blade (formely), Cordak Blaster|
|Matoro, (former deputy leader; deceased) Toa of Ice||Tryna, the Great Mask of Reanimation||Twin Cutter, Cordak Blaster|