The Ignika sinks to the Pit and is found by the Mahri Nui Matoran. However, the Barraki intends on taking the mask so they can escape the Pit as air-breathers, thus a siege was made against Marhi Nui. Just as the Barraki get it, the mask unleashes a great wave of energy.

At the same time, the Toa Inika are in the Pit from the Cord and is transformed into the Toa Mahri. Meanwhile, the Barraki get the mask and call off the siege, leaving some units at the airweed fields. Hydraxon is also created from Dekar by the Ignika, and he goes on a quest to recapture all prisoners.

The Mahri, except Matoro, meet the Mahri Nui Matoran and pledges their help to them. Matoro is captured by Hydraxon, and leaves him guarded by Maxilos and Spinax. Soon, Makuta reavels himself as the possessing Maxilos and frees Matoro, for he, surprisingly, is on the Mahri's side to get the Ignika.

The Toa Mahri and Barraki meet and after a few moments of no violence, battles erupts between the two. Also, Hydraxon manages to get the Ignika from Nocturn (affliated with the Barraki) and attempts to destroy the mask (when he was Dekar, he intended to destroy it, so memories of that still remain). Hahli manages to save the Ignika, but it falls in the hands of Mantax.

Mantax flees to the Barraki fortress and orders a meeting with the group, discussing about a traitor amongst the group. When confusion erupts later, Takadox reveals himself as the traitor with a knife to Mantax.

The Mahri evacuate the Matoran to Voya Nui, encountering the mutated Piraka. Axonn comes and defeats them and gives the Toa a vehicle to get back to the Pit.

Back there, the Mahri wages battles against Barraki, Rahi, and more. Finally, Matoro gets the mask, the Cord is destroyed, and Voya Nui is heading to the universe core. However, Mata Nui had died so gloom and doom is nigh ...

... but Matoro knows all hope isn't lost; he follows the island while the Mahri hold off the Barraki. He manages to get to the universe core and dons the mask to revive Mata Nui, while he "dies" by becoming pure energy.

This event teleports the rest of the Mahri to Metru Nui as air-breathers. There, Vakama notifies them of Matoro's death.

Elsewhere, the Toa Nuva gain new armor from Artakha and now are on a new quest to Karda Nui!