With the stories of the Turaga about Metru Nui before and after the Great Shadow, all inhabitants of Mata Nui go back to Metru Nui, and are greeted by Turaga Dume himself. In a meeting with the Turaga and Toa Nuva, they find out that Mata Nui (the spirit) is slowly dying. The Toa Nuva are sent on a quest to Voya Nui to get the Mask of Life to save Mata Nui, getting there via canisters Dume built while everyone else was on Metru Nui.

Meanwhile, the group known as Piraka have already landed on Voya Nui using the Toa Nuva's original canisters (the ones they had pre-Toa Nuva), and convince the Matoran on the island that they are Toa. They make the Matoran to drain Mt. Valmai to get to the Mask of Life's chamber to get the mask for their own self-greedy ambitions. Course, thoughout their time there, betrayal is apparent and imminent if one gets the mask, even with partnership. Course, the working Matoran isn't fast enough, so Zaktan of the Piraka uses Antidermis to enslave all to work harder but 6: the Voya Nui Resistance Team.

Now the Toa Nuva reach Voya Nui, and fight the Piraka, with the Piraka beating them despite certain problems. They take the Toa to the mountain to be engulfed in the lava. Fortunately, the Toa Nuva escape, but get into a fight with the Resistance team, but they manage to find out whose side they're on, so they team up for another attack on the Piraka. When they get to them, the Order of Mata Nui member Brutaka has joined the Piraka. He defeats the new team in one attack, strengthened by Antidermis. Brutaka then takes custody of the Toa Nuva while the Piraka does the same with the Resistance Team.

Now, back on Metru Nui, Nokama has told Jaller about Mata Nui dying, so he, Matoro, Hewkii, Nuparu, Hahli, Kongu, and Takanuva head to Voya Nui. They get to Karzahni and Takanuva can't get into there, but the Matoran can. Takanuva goes back to Metru Nui as the others get further in Karzahni, where they meet the ruler himself. He makes them change their masks and force them to work in his realm. Matoro's quick thinking of using Karzahni's own mask on him gave them time to get into canisters and head to Voya Nui.

Reaching Voya Nui, the Red Star strike lightning on the canisters, changing the Matoran into Toa Inika. They test out their abilities and meet up with the Resistance Team who managed to escape the Piraka. Joining up, they meet Axxon, another Order of Mata Nui member and former friend of Brutaka and fight the Piraka and eventually find the chamber to the Mask of Life.

In the chamber, both Piraka and Toa Inika brave through the defenses set up by the Mask of Life (exluding Umbra, who was sent there). Both reach where the mask of life was: on Vezon (clone of Vezok), riding on Fenrakk. The Piraka first loses to him, then the Toa Inika continues off the Piraka to fight Vezon.

Meanwhile, Axxon and Brutaka fight each other, Axxon trying to convice Brutaka to renounce his betrayal, to no avail. Brutaka is defeated by Axxon and then Botar comes to take Brutaka to The Pit for his betrayal. During the previous battle, the Antidermis vat is destroyed.

With the Resistance Team, they rescue the Toa Nuva and brief them about the Toa Inika.

The Toa Inika manages to get the Mask off Vezon after Fenrakk became the Kardas Dragon (well, Matoro did). Kardas makes one more blast at Matoro, making him lose the mask as it flies away out of the chamber and into the water. Hahli attempts to get it, but because she doesn't have the mask of underwater breathing, she almost drowns, but a Matoran of Mahri Nui saves her but dies when he reaches the surface. Before he dies, that Matoran pleads the Inika to save the city of Mahri Nui which was underwater and used to be a part of Voya Nui.

Now, the Resistance Team, Toa Inika, Toa Nuva, and Axxon discuss what to do. Axxon and the team would rebuilt the island, the Toa Nuva would return to Metru Nui, and the Inika would go get the mask. When the Inika leaves, the Toa Nuva reveal that they were lying about getting back to Metru Nui, instead having a new quest to prepare the awakening of Mata Nui.

Meanwhile, Karzahni is planning to go to Mahri Nui, as will Makuta, who was actually the Antidermis (or at least its essence). The Mask of Life continues to sink towards Mahri Nui as well.