Makuta, the Master of Shadows, remains imprisoned in a crystal prison after the events of the previous film. A mysterious figure speaks Makuta’s name, scratches the prison, and pulls out a shard. This figure is Roodaka, queen of the Visorak horde, who implants the shard as a heartstone and vows to free Makuta.
Vakama, a Turaga, narrates the tale of the Toa Metru. The Toa Metru — Nokama, Matau, Onewa, Whenua, and Nuju — left Metru Nui after using their elemental powers to seal Makuta in protodermis, vowing to return to rescue the Matoran they left behind. In their absence, Metru Nui falls to the Visorak horde under Sidorak and Roodaka.
The Toa Metru arrive on the shore of Metru Nui and approach the Coliseum where Matoran are kept, only to be ambushed by Visorak and captured. They are brought to the Coliseum, where Roodaka suggests they are infused with the Visorak venom and mutated into beast-like forms. Ordered by Sidorak to be killed, the Toa are sent plummeting to their deaths, but are saved by six flying Rahaga led by Norik.
In a crucial revelation, Norik explains that the Visorak venom mutates the Toa into Hordika, keeping them in their beastly states unless the venom is neutralized in time. Their only hope to return to normal is an ancient hermit-like Rahi named Keetongu—a figure many deem a myth. Vakama grows agitated over the mounting blame, storms off, and attempts to rescue the Matoran alone, only to be captured again. Roodaka takes advantage of his anger by offering a deal: if he leads the Visorak horde, he can rule Metru Nui.
The other Toa and the Rahaga journey to the Great Temple in Ga-Metru to seek clues to [Keetongu]’s whereabouts, and eventually the hermit agrees to aid them. The party returns to the Coliseum to challenge the Visorak. Matau confronts Vakama, while [Keetongu] goes after the king and queen. Roodaka orchestrates the death of Sidorak by leaving him to be killed by Keetongu. Matau tries to reason with Vakama, apologizing for doubting his leadership and reminding him of his duty and destiny to rescue the Matoran.
Norik frees his fellow Rahaga and joins the Toa, but Roodaka arrives and demands control over the Toa’s elemental powers. Vakama and Matau rejoin the team, with Vakama feigning continued loyalty to Roodaka. After the others fail to defeat Roodaka with their elemental spinner weapons, Vakama reveals his true change of heart and orders the Visorak to depart and be free; the horde obeys. Unaware that Roodaka’s heartstone is the shard Makuta’s prison, Vakama then fires his own spinner at it, inadvertently breaking the seal and freeing Makuta. The Master of Shadows uses his powers to teleport the incapacitated Roodaka to safety. Norik, fully understanding the gravity of the moment, keeps vigil as Makuta vents his newfound freedom, while Keetongu restores the Hordika to their Toa Metru forms. The Toa bid farewell to the Rahaga and depart Metru Nui with the Matoran, hopeful yet wary of the challenges ahead.
Turaga Vakama concludes the story he had been recounting to Takanuva, Jaller, and Hahli after the events of the first film. As they walk away, he tells them that it is time for them to discover their own destinies.
