Upon his defeat, Makuta released the ancient Bohrok. Bohrok are robotic drones that were designed to "cleanse" the island of Mata Nui to its state "in the before-time". The Bohrok began to tear through the villages on the island, forcing Matoran to flee. One inventive Matoran of Earth, Nuparu, builds a powerful vehicle called the Boxor, made from parts of a damaged Bohrok in order to fight off the swarms. The Toa, unaware of the Bohrok's purpose, collected the Bohrok's Krana (mask-like creatures that function as their brains) to confront the Bohrok Queens, the Bahrag: Cahdok and Gahdok. The defeated Cahdok and Gahdok are sealed in a prison created by the Toa's elemental powers. The Toa Mata are then exposed to a substance called Energized Protodermis, which transforms them, granting them new armor and weapons. They renamed themselves the "Toa Nuva".
With Cahdok and Gahdok defeated, the Bohrok Swarms are stopped and returned to their hives. However, six new elite Bohrok, called the Bohrok-Kal, appeared with the purpose of releasing the Bahrag. They then proceeded to steal the Toa Nuva's powers, which are the key to breaking the seal. On the verge of defeat, the Toa force all of their powers into the Bohrok-Kal, overloading and defeating them.
Shortly afterwards, two Matoran, Takua and Jaller, discovered the Kanohi Mask of Light. They were tasked with traveling across the island of Mata Nui to find the Toa of Light. Meanwhile, Makuta created and sent out six creatures called Rahkshi to find the mask and stop the coming of the Toa of Light. The Rahkshi tore across Mata Nui, destroying the villages of Ta-Koro and Onu-Koro. The Rahkshi were stopped by the Toa, but not before killing Jaller. Jaller's death caused Takua to realize he was the Toa of Light, and he donned the mask to become Toa Takanuva. Takanuva went to confront Makuta and, during their battle, they both fell into a pool of energized protodermis, a silvery substance with the power to change or destroy a being, and became fused together into the being Takutanuva. Takutanuva then proceeded to open the door to the city of Metru Nui, allowing the Matoran and Toa through. Using some of his life energy, he revived Jaller while still holding the door open. However, the use of energy was too great and Takutanuva was crushed by the door, seeming to kill both Takanuva and Teridax, leaving only Takanuva's Mask of Light. Takanuva was promptly revived when his mask was used to activate the beacon to Metru Nui. Afterwards, the Matoran prepared to return to the island city of Metru Nui.
As the Matoran prepared to journey to Metru Nui, the Turaga (village elders) revealed that they had once been Toa, fighting in Metru Nui against threats such as the Morbuzakh plant creature and the Dume-controlled Vahki enforcement squads. They, as Matoran, were transformed into the Toa Metru by Toa stones containing power sacrificed by Toa Lhikan. Their mission was to find the six Great Disks and defeat the Morbuzakh, a plant menace that threatened to destroy the city. When they did, however, they were betrayed by Dume, the Turaga of the city. Later, they discovered that Makuta Teridax had taken the disguise of Dume and taken control of the Vahki (law enforcement robots). His plan was to put the Matoran to sleep, wipe out their memories, and reawaken them "as their conqueror." The Toa fled, but were attacked by Teridax. Combining their elemental powers, they were able to seal Teridax in a prison of crystallized protodermis. The Toa traveled to a new island, which would later be known as Mata Nui, vowing to return to save the Matoran.
They do return. However, the evil king Sidorak and his viceroy Roodaka had been reigning on the island, with vicious spider-like creatures called Visorak. The Toa were soon captured and mutated into bestial Toa Hordika. To revert to normal, the Toa sought out the legendary Rahi Keetongu. Toa Vakama, however, betrayed the other Toa and joined Sidorak, who made him the leader of the Visorak. The other Toa confronted the Visorak horde in a great battle, and convinced Vakama to rejoin them. Vakama then ordered the Visorak to be free. Keetongu then killed Sidorak, whom Roodaka and Vakama betrayed. The six Toa then defeated Roodaka with all six of their elemental powers. However, this had the side effect of freeing Makuta because Roodaka carried a fragment of his prison. The Toa struck her for this reason. Having been restored by Keetongu, the Toa Metru brought the Matoran to a new island. When they sacrificed their power to awaken the Matoran, they become Turaga, and later established new villages on this island called Mata Nui.
The Toa Nuva learned that Mata Nui was not only asleep but dying. To save him, they must travel to the island of Voya Nui and seek the mysterious Kanohi Ignika, the Mask of Life. The Toa Nuva set out on this adventure but are quickly taken prisoner by six new and powerful enemies, the Piraka: Zaktann, Hakann, Vezok, Thok, Reidak, and Avak. They sought the mask for their own dark purposes. When the Toa failed to return, a group of six Matoran followed after them. Jaller, Hahli, Hewkii, Nuparu, Kongu, and Matoro escaped to the island in Toa canisters, but as they traveled, bolts of lighting from the Red Star transformed them into the Toa Inika. Upon their arrival, they learn of the Piraka and how they enslaved the local Matoran by posing as false Toa, in order to make the Matoran build them a fortress. With the help of a small Matoran Resistance and the ancient guardian Axonn, the Toa Inika were able to free the Toa Nuva, find the temple of the mask, and battle the Piraka as well as the other creatures guarding it. They eventually emerged victorious with the Kanohi. But the Mask of Life possessed a will of its own, and in the last moment evades them all, rushing into the depths of the sea.
Following the chase for the Mask of Life, the Toa Inika descended into the waters after receiving the mysterious clue "save the sunken city" from an unknown Matoran, who had saved Hahli from drowning at the cost of him dying from decompression sickness.[14] A burst of energy from the Mask of Life transformed the Toa Inika into water-breathing forms. They discovered an inhabited village of Mahri Nui that had broken off from Voya Nui and sunk a thousand years ago. The village was threatened by ancient warlords known as Barraki that had been mutated by the nearby mutagenic waters called "The Pit". The Toa, now known as Toa Mahri, faced off against the Barraki to survive. However, by the time the Toa retrieved the mask, the Great Spirit died. Realizing there was still hope, Toa Matoro rushed to the core of the universe and sacrificed his life to revive Mata Nui. In the last moments of his life, Toa Matoro used the Mask's power to teleport the Toa Mahri back to Metru Nui and allow them to breathe air again. The Great Spirit's life was saved but he still had to be awakened.