On a tropical Island called Mata Nui, six Toa heroes wash ashore in six Toa Canisters. After building themselves up, they discover their Kanohi masks and their elemental powers: Fire, water, stone, earth, air and ice. The Toa, named Toa Mata, each meet the Turaga, the elders of each village, or Nui, on Mata Nui. Eventually, they meet each other and discuss the next course of action. They begin to search their own five other masks, hidden on Mata Nui. Each mask that they found had the powers of one of the other Toa Mata's masks. They encounter dangerous Rahi, animals which attack them during their quest, and learn about Makuta Teridax. As the Toa collected their masks, they head for Kini-Nui to receive their Golden Kanohi which give them the abilities of all six masks in one mask, without the need to summon the other masks of power. They travel to Mangaia, Makuta's lair, to face him. The Toa Mata fuse together to form Akamai and Wairuha, battling a horde of Manas as they move towards Teridax. Being seperate again, they begin to battle Makuta in his Vortex form, one of his many forms he can take. But the Toa don't manage to defeat him and are teleported to Kini-Nui again. Takua, who followed the Toa, discovers the Bohrok as they begin to hatch. He escapes to the Ta-Wahi beach.

Insectoid creatures called Bohrok are awakened and rampage over Mata Nui to destroy everything they can see. The entire village of Le-Koro is overrun by the Levahk, who replace their masks with Krana, living beings which control the Bohrok or the wearer. Lewa hears the news of his village being overrun and goes to help. He soon discovers it is a trap as Turaga Matau greets him by replacing his Mask of Power with a Krana. Lewa and the village are saved by Onua and a group of Onu-Matoran in Boxor vehicles, built from Bohrok parts.

The Toa originally believed that the Bohrok were otherworldly beings. However, when Tahu and Kopaka discover and enter a Bohrok nest, they discover that the Bohrok came from under Mata Nui. They leave to join with the other Toa and enter the Bahrag's lair. By placing all collected Krana in special niches, the Toa Mata unlock a passage to six Exo-Toa, armored and armed suits that the Toa can wear. They begin to battle the Bohrok queens Cahdok and Gahdok, but soon realize that the suits hinder their elemental powers, which they need to defeat the queens. After shedding their armor, they manage to defeat the Bahrag by encasing them in Protodermis. Suddenly, the ground begins to move and the Toa fall into energized Protodermis, transforming them into Toa Nuva, improved forms of themselves. They manage to escape the collapsing roof.

After the Toa Nuva imprisoned the Bahrag queens, six elite Bohrok, called Bohrok-Kal, are awakened and plan to defeat the Toa Nuva. They steal their Nuva symbols, which results in the Toa Nuva losing their elemental powers. The Toa find out on the new group of Bohrok and join together to recover another six sets of Kanohi masks. They battle the Bohrok-Kal, Lewa, Gali and Kopaka even merging into Wairuha Nuva to stop three Bohrok-Kal. But they also merge into a Kaita, Bohrok-Kal Kaita Ja, and defeat the Toa.

The Bohrok-Kal eventually travel to the Bohrok Nest with the Nuva Symbols. The Toa follow them and witness the Exo-Toa fighting the elite Bohrok to guard the Nuva Cube. The Exo-Toa are defeated and the Bohrok-Kal are ready to fit the Nuva symbols onto the Nuva Cube to awaken the Bahrag and release the Bohrok swarms again, just as Tahu uses the Kanohi Vahi to slow down time around the Bohrok-Kal. But their Krana-Kal turn silver, protecting them from this threat.

The Toa Nuva then let their powers flow through their Nuva Symbols, increasing the powers of the Bohrok-Kal. But that power is too much for them and they are destroyed by their own power. The Toa recover their symbols and the Krana-Kal and leave the nest.

The Matoran celebrate Naming Day and rebuild themselves from their old, small to a bigger, stronger body. Takua and Jaller discover a carved stone in an underground cave and melt it in lava, revealing the Mask of Light. He hands it to the Turaga, who tell them they have to go on a quest to find the seventh Toa, the Toa of Light. Makuta, sensing this event, releases six Rahkshi to stop the pair finding the seventh Toa. Shortly after leaving Ta-Koro, the Rahkshi attack the village, destroying it and poisoning Tahu.

Meanwhile, the two travel to Le-Wahi and are attacked by an ash bear, but are saved by Lewa. He travels with them to Ko-Wahi and they meetKopaka, but the Rahkshi arrive and the three have to flee. Kopaka defeats them by plunging them into a sea and freezing it. The pair travels to Onu-Koro, where Takua meets Teridax, who tries to convince him to give him the mask. Takua refuses and joins with Jaller but due to a misunderstanding they part and go separate ways. As Jaller arrives in Onu-Koro, the Rahkshi Kurahk, Vorahk and Turahk attack the village. Takua notices this and joins Jaller to flee. The Toa Nuva join the fight against the sons of Makuta. Tahu gets hit by Kurahk's staff and turns against the Toa, just before Kopaka freezes him. They can stop the Rahkshi for a short while and flee Onu-Koro too.

In the jungle, Kopaka and Gali manage to cure the poisoned Tahu Nuva. In the meantime, Takua and Jaller reach the Kini-Nui temple and are ambushed by three Rahkshi. The Toa arrive and begin to battle them. Jaller sacrifices himself from preventing Turahk attacking Takua. Takua puts on the Mask of Light and transforms into Takanuva, the Toa of Light. He easily destroys the Rahkshi and builds himself a vehicle to travel to Makuta's lair. Inside, he battles Teridax in a Kolhii match. In a struggle, they both plunge into a pool of energized Protodermis. Takutanuva is created, opens the gate to Metru Nui, the city beneath Mata Nui, and brings Jaller back to life. As soon as everyone is on the other side of the gate, the weak Takutanuva lets the gate crush him. Only the Kanohi Avokhii remains and Makuta is thought to be dead.