Going back from the island of Mata Nui to Metru Nui, the Toa Metru sail on a Vahki Transport. They made it, but their transport sunk. On Metru Nui, they see the total chaos of the area (buildings destroyed, Rahi from the Archives escaped, Visorak webbing). They soon get captured by the Visorak, mutated into Toa Hordika, and saved by the Rahaga. With that, they have to deal with their changed selves. Vakama feels guilty to have been responsible for this and betrays the rest to Roodaka, viceroy of the Visorak. Vakama then captures all of the Rahaga except Norik and takes them under the custody of the Visorak. Meanwhile, the rest of the Toa Hordika and Norik go look for Keetongu for help. They succeed, but it refuses to revert the Toa back into their old selves, but will help them get rescue the other Rahaga and Vakama. The group goes to the Collesium to attack the Visorak armies, fighting a great battle. In the end, Vakama comes back with the Toa, the other Rahaga are saved, the Visorak are freed, Sidorak, king of the Visorak, is killed. Roodaka manages to free Makuta of his prison, and he uses a dark claw to wisk her away. Keetongu then restores back into Toa Metru, and all of them help get Matoran pods into Airships to fly to Mata Nui.

Other Info:
Vakama manages to get the Vahi that was lost previously.
The Avohkii and Mahoki Stones come into significance in the middle of the storyline.
Krahka and Tathorak ally with the Toa to fight the swarms. They both get into the Zone of Darkness with Zivon.