The Matoran Universe is now a dark and dangerous place, home to the peaceful Matoran and their leaders, the Turaga. But as of late, a perilous and treacherous being called Teridax has threatened the island of Mata Nui, now the centre of all life and activity in the Matoran Universe. Teridax, part of an alliance called the Brotherhood of Makuta, has cast the Great Spirit, which was protecting the civilians of the Matoran Universe, into a great slumber.
But luckily, at the dawn of the time, six Toa were built and trained to guard the Great Spirit, Mata Nui. They were put in stasis inside Canisters only to be released when the Great Spirit needed them most. They were built as a failsafe.
And now, the Great Spirit is dying. The six Toa wash ashore on the island of Mata Nui with a purpose to discover. Once they find out that their duty was to stop Teridax's threat, they intend to do so. In their second face-off with Teridax they unlock their pure powers of unity and trap Makuta in a Protodermis crystal.
However, their celebrations are cancelled when a crack is discovered in the Protodermis crystal and six shadows emerge from it, forming Makuta's sons, the Rahkshi. Their only goal is to release their "father" from the Toa's trap, and after a struggle, this happens. Instead of gratitude, Makuta drains the life force from his Rahkshi to grow stronger and mutate himself into a much more dangerous being.
As Teridax unleashes a much worse threat to the Toa, they are seriously injured and their bodies are rendered useless, and are presumed dead. However, seven Matoran (Takua, and six others from each Koro) unite when they discover that the Toa are still alive. Nuparu, Onu-Koro's greatest engineer, builds new and more powerful bodies for the Toa and they transport the Toa's functioning heartstones to their new bodies, thus creating the Toa Nuva. The Toa Nuva face off with Teridax and stop him from completely destroying the island.
While Teridax recovers, Takua stumbles across the Mask of Light on one of his journeys. When Teridax senses that the Kanohi Avohkii has been found, he revives his Rahkshi but mutates them into the Rahkshi Kaita, and orders them to destroy the Mask and its owner. Meanwhile, Takua and Jaller set off on a journey to find the Seventh Toa, who is the supposed owner of the Mask of Light, and also the only one who can destroy all evil on the island of Mata Nui. On their journey, they are attacked by the Rahkshi Kaita. When the Toa arrive, Jaller has already died, and Takua has put on the Mask of Light, turning into Takanuva.
In Mangaia, Teridax senses Takanuva's birth, and decides that only he has the ability to destroy the Mask of Light, so he leaves Mangaia to fight Takanuva. During the fight Takanuva is injured to the point of dying, but Tahu saves him and is nearly killed himself. Takanuva unlocks the true powers of his Mask of Light and creates his Staff of Light, which he pounds on the ground to evaporate all of the evil inside of Teridax (and as Teridax is pure evil, it kills him).
Five years later the inhabitants of Mata Nui have traveleld to Metru Nui due to the ravaging of their homeland was too severe to be fixed. As they travelled to the City of Legends they watched their island crumble to dust. A distress signal was received from Voya Nui and the Toa were sent there to solve the problem. Back in the present the Toa haven't returned. Takua's team that revived the Toa Mata into the Toa Nuva (Jaller, Hahli, Nuparu, Kongu, Matoro, and Hewkii) decide that something has happened to the Toa and the Turaga aren't telling them. Despite multiple attempts to extract information from their Turaga, the Matoran decide to travel to Voya Nui and find out for themselves. At first Takanuva warns them of their dangerous journey, but when they ignore him, the Toa of Light doesn't try to stop them.
During a storm the Sea of Protodermis changes the course of the Matoran's canister and they arrive on the island of Karzahni. There they are painfully stripped of their Masks and given new ones which represent their belonging to Karzahni, the ruler on that island. The Matoran plot an escape, and it involves Nuparu's engineering skills to make a device which will stun Karzahni. When it is ready, the device explodes and kills Karzahni, which wasn't what they intended to do, but they escape anyway.
When they arrive on Voya Nui, they are "kidnapped" by Balta. Balta explains the happenings on Voya Nui: How the Piraka arrived and claimed to be Toa heroes, how they then enslaved the Matoran, how they came for the Kanohi Ignika, Mask of Life, how the Toa Nuva arrived, and how the Piraka caught them and are keeping them locked up in a room designed for torture. The Matoran agree that they should go and rescue them, but they don't have anything that could aid them on their quest. During a journey for materials, they are attacked by Piraka Reidak. The Matoran run from his untilt hey reach the Canister they arrived to the island in. They close the lid to try and hide, but Reidak tears it open. All of a sudden a storm breaks out and a bolt of red lightning hits and explodes the Canister, injuring Reidak (but unfortunately not killing him) and mutating the Matoran into the Toa Inika. The Toa Inika then went after the Piraka, only to find that they weren't in their fortress. They free the Toa imprisoned there who are too injured to help the Toa Inika on their quest to defeat the Piraka (despite arguing about it). The Toa Inika then head into Mount Valmai, where the Piraka are searching for the Mask. They face off with Umbra and finally witness the Piraka about to enter Vezon's lair. They face off in a massive battle where some of the Piraka kill themselves, and some Toa have to kill the last Piraka in self-defence. When they enter Vezon's lair, they fight off Vezon and Fenrakk. However, Fenrakk is pushed into the lava and mutated into the Kardas Dragon. Vezon defeats the Toa due to their exhaustion after the battle against the Piraka. Hahli, Kongu, Hewkii, and Nuparu are captured. Jaller and Matoro then plan a rescue mission. They break in and Jaller frees their friends while Matoro faces off with Vezon. Matoro tears the Mask of Life off of Vezon's face, and the separation of it kills Vezon. The Kardas Dragon, who can't live without Vezon, dies as well. After the struggle, Jaller and Hahli find out that they love each other.
The Toa Inika then assemble a Canister for all 12 Toa to travel back to Metru Nui in, but the Ignika glows and launches itself into the sea and towards Mahri Nui. Despite the Toa Nuva's protests, Jaller sends the Canister away to Metru Nui.
The Toa Inika then travel to Mahri Nui via The Cord, where an energy pulse of the Kanohi Ignika mutates them into the Toa Mahri. When they arrive in Mahri Nui, they fight and defeat Pridak who is currently Mahri Nui's only threat. But Pridak then escapes and recruits the Barraki Warlords, who are also searching for the Mask of Life.
Makuta Maxilos is then found by Matoro, and Hydraxon attempts to steal the Maks of Life. Matoro has a vision of his destiny, having to put on the Mask and kill himself, and only tells it to Hahli, who feels for him, and they end up kissing. Jaller catches them and confronts Hahli about it, ending their relationship despite Hahli's protests. In the final battle for Mahri Nui, the Toa Mahri fight the Barraki and Jaller fights both Hydraxon and Makuta Maxilos for the Mask of Life. Jaller is injured and Matoro rescues him and the Mask of Life. Matoro then races to the falling island of Voya Nui while being chased by Takadox. When Matoro puts on the Ignika and dies, the energy pulse converts him into Toa Ignika and kills Takadox. Jaller then realises why Hahli was with Matoro and forgives her. They then escape to Metru Nui and let Hydraxon hunt down and jail the other Barraki. Pridak is the only one who survives the hunt. When the five Toa Mahri arrive to Metru Nui, the Toa Nuva have been rebuilt as their wounds were too fatal. The Toa Nuva are then sent to Karda Nui, the Core of the Matoran Universe, to find the Mask of Creation.