A new darkness is rising; the Skull Spiders have overrun Okoto, searching for the legendary Masks of Power. In desperation, the Protectors retreat to the Temple of Time, and recite the Prophecy of Heroes, learned in ancient times from the lifeless body of Ekimu. Six Toa then rain down upon Okoto within comets. It is their destiny to save the island from evil.
Fallen from the stars, Tahu encounters Narmoto and his villagers. Unsure of who he is, Tahu is explained his destiny: to retrieve his Golden Mask of Power and save the island from evil with his fellow Toa. Tahu single-handedly defeats a group of Skull Spiders, confirming Narmoto's beliefs and earning the villagers' awe and respect.
The Toa journey through Okoto’s toughest regions in order to reach the shrines of the golden masks: Lewa cuts through the dense jungle, Pohatu treks through blistering deserts, Kopaka fights against the raging blizzard, Gali swims through currents, and Onua drills his way through solid rock, all in order to claim the Golden Masks of Power. Nearing the Golden Mask of Fire, Narmoto warns Tahu that they will face more dangers, as the Skull Spiders are following closely behind.
The Toa brave the wilds of Okoto, with their Protectors guiding them, in order to retrieve the Golden Masks of Power. Tahu and Narmoto ascend a temple in the Region of Fire, closely followed by a horde of Skull Spiders. While Narmoto uses his Elemental Fire Blaster to fend them off, Tahu surfs into the caldera to reach the Golden Mask of Fire.
While the Protectors hold off hordes of Skull Spiders, each Toa reaches his or her Golden Mask and puts it on. Narmoto is overwhelmed by Skull Spiders, and tells Tahu to run, but Tahu unleashes the power of the Golden Mask to defeat the Skull Spiders. The other Toa do the same, saving their Protectors from the Skull Spiders.
The six Toa, having claimed their individual golden masks, fend off hordes of Skull Spiders. Tahu assumes his quest is finished, but then receives a vision from Ekimu, and is told that he must travel to the City of the Mask Makers in order to awaken the Mask Maker. Tahu asks if he must do the task alone; Narmoto tells him of the other five Toa heroes, and that they must follow the visions from the masks quickly to defeat evil.
The five remaining Toa - Gali, Lewa, Onua, Pohatu, and Kopaka - unite at the City of the Mask Makers, where they encounter Tahu, who introduces himself as their leader. Lewa is amused by this prospect, while Kopaka challenges his claim. The Masters of Ice and Fire begin fighting; when Gali is unable to stop them, Onua steps in and physically separates the two. Lewa jokingly claims Onua would be a better leader than either. Pohatu quickly quiets the group, having sensed the approach of the Lord of Skull Spiders.
Several of the Toa try and fail to defeat the Lord of Skull Spiders on his or her own. Onua urges them to work together, and the Toa unleash a barrage of attacks that overwhelms the Lord of Skull Spiders. Onua then collapses the portion of the bridge beneath the Lord of Skull Spiders, dropping it into the chasm.
Pohatu spots an empty pedestal on the bridge. The Toa receive another vision from Ekimu, congratulating them on their victory and imploring them to find his body. They cross the bridge and enter the ancient city, with Lewa scouting ahead. Onua trusts the masks to guide them, but Pohatu expresses a feeling of foreboding about the city. As the Toa move through the city, a skeletal hand breaks through the ground behind them.
The Toa enter the City of the Mask Makers. Tahu accidentally springs a trap that seals them in, and the group is ambushed by a horde of Skull Warriors. While Tahu and Kopaka bicker about leadership, Lewa flies off to scout ahead, leaving the other Toa to fend for themselves. Onua, attempting to prevent the Skull Warriors from keeping them in the city, accidentally collapses the bridge they took in, inadvertently forcing the Toa to stay.
Lewa returns from scouting, knocking the Skull Warrior archers from their vantage point, allowing the rest of the Toa to beat the Warriors on the ground. When questioned by Kopaka, Lewa reveals that he spotted an Arena, which he thinks would be a "fun" destination. Kopaka refuses to allow him to visit, though Lewa ignores Kopaka's directives and heads to the Arena alone. There, Lewa is confronted by Skull Slicer, who steals his mask and leaves his unconscious body for the other Toa to find.
The Toa follow Skull Slicer into the Arena, where they witness him don Lewa's golden mask and begin to drain it of energy. Pohatu explains that there is a link between the Masters and their masks, which is the energy the Skull Creatures are after. A barely conscious Lewa informs the Toa that to win the game, they need to hit a lever. Kopaka, Tahu, and Pohatu defend Onua as he smashes the lever and dispatches Skull Slicer. However, the damage done collapses the arena.
Trapped underneath the rubble of the destroyed Arena, the Toa reflect upon their mission and what led them to Okoto. After remembering the way the Protectors guided them in their task, the Toa find a renewed sense of purpose in saving the island. Lewa detects a breeze nearby, indicating that there is a tunnel they can use, and Onua destroys the rocks pinning them down.
The Toa emerge from the underground tunnel into a graveyard, and begin searching for Ekimu's tomb. Lewa notices a large mausoleum emblazoned with the Mask of Creation, and the Toa head for it. Tahu steps on a bone, alerting their presence to a pair of Skull Scorpios, who steal Pohatu's mask and defeat Gali, Tahu, and Onua. Pursuing Lewa, the Scorpios hesitate briefly at the entrance to Ekimu's tomb, but press on.
The Skull Scorpios advance toward Ekimu's tomb, but Lewa manages to cut a stone with the Mask Maker symbol, burying them and recovering Pohatu's Golden Mask of Stone. Inside the tomb, the Toa find Ekimu's body and, through their masks, he tells them to use their elemental powers to awaken him. The Toa use their powers and Ekimu finally rises from his slumber.
The newly awakened Ekimu berates the Toa for having arrived too late, as Kulta, the Skull Grinder had recently claimed the Mask of Creation, and will be attempting to destroy it. Surveying the ruined City of the Mask Makers, Ekimu laments the damage done, which Lewa prevents Onua from taking credit for. Ekimu claims that Skull Grinder will be heading to the Forge, which is the only place the Mask of Creation can be destroyed.
Ekimu leads the Toa to the forge, where Kulta is inside preparing to destroy the Mask of Creation. Tahu and Kopaka get into another argument entering the forge, while Onua is quickly taken out by Skull Basher. Despite being down one member, Ekimu rallies the Toa to work as a team and defeat Basher. Inside, Kulta puts on the Mask of Creation, and challenges the Toa; Ekimu requests them to distract Kulta while he completes another task.
Empowered by the Mask of Creation, Kulta fells all six Toa in a single blow, breaking their Golden Masks in the process. Despite being weakened and outmatched, the Toa rally themselves long enough to halt Kulta's progress, giving Ekimu enough time to recreate his Hammer of Power. Ekimu uses the hammer to knock the Mask of Creation off of Kulta's face, defeating him. In the aftermath, Ekimu reforges the Toa's masks and commends them for proving their worth.