, the leader of the Av-Matoran, became corrupted, along with many others. Even , hero of the Av-Matoran, succumbed to the attack of the enemies, who Kirop revealed before his corruption to be members of the . All of the Av-Matoran villages fell save one, where the remaining uncorrupted Matoran were sheltering at the time of 's death. Minutes after the tragic event, Tanma noticed falling down the waterfall and there was suddenly a gigantic explosion of light, blinding the three attacking Makuta (, , and Chirox) and bringing the back to life. Likely Tanma ordered all the other Matoran to duck and close their eyes.
A few hours later the Av-Matoran waged a battle against the Makuta and the Shadow Matoran in the sky. And as they did so, the arrived in Karda Nui, teleported there by from .
As soon as the Toa Nuva arrived, Pohatu rushed to engage the Makuta in battle. Wise Onua was the one that noticed that the bat-like Makuta were blind. The Toa helped the Matoran finish the fight and regrouped at the village, where they began to remember that they once lived in Karda Nui. They discovered the use of , which they named Midak Skyblasters. (Midak was the name of a strange of who liked the light despite being able to see better in the dark, and had always wanted a weapon called a "Skyblaster", and none of the other Toa cared to object, thus the name was created.)
Meanwhile in the 's Shadow Leech hive, and were working on a new experiment, a Rahi that could turn into a liquid when disturbed. Mutran "kept slipping in it" and ordered Vican to get rid of it. He kicked it out of the hive and it fell into the swamp below, only for Vican to notice too late that it had begun to fly.
Vamprah arrived at the hive and forced Mutran to come to the main Makuta lair to create a flying Rahi to take Vican to to summon . He created a part-Rahi and part-Matoran creature, and sent Vican off to Destral.
Back at the Av-Matoran's village, the Toa Nuva learned of Matoro's death from the Av-Matoran's description of the events leading up to the blinding flash of light. From this they realized that the that Matoro was last seen with was probably in the swamp below. , , and departed for the swamp and , , and stayed to defend the Matoran. Tahu leading one group and Kopaka leading the other.
Later, an Av-Matoran who looked up to the Toa, named , approached Kopaka and gave him part of an object called a . It was a tablet detailing how to awaken Mata Nui from his endless slumber, but it had been broken into six pieces. According to Solek, the Makuta held two pieces (one held by ), and the locations of the other three were unknown. Kopaka, understanding all that these Matoran have been through, spoke kindly to him and gave him inspiration for the battle to come, using how Takua became a Toa as an example. It was then that Kopaka learned that Solek knew Takua.
The next day, Lewa happened to knock Kirop out of the sky in battle. Kopaka captured him and with Lewa's help, led him to believe the Toa would be launching an attack on the Shadow Leech hive in a few hours. Kirop found a way out and escaped to the Shadow Leech hive, exactly as the Toa had planned. They followed him, along with Tanma, Solek, and another Av-Matoran named .
In the swamp at the bottom of Karda Nui, the Mask of Life pondered whether or not to create some more guardians for it. But recalling the failures of others like and the gigantic , it decided to create a body for itself, so it could have friends like its former guardian, Matoro.
It also created itself a Skyboard. It flew into the skies above and began silently following Kopaka and the others as the trailed Kirop. It (now considering itself a "he") proved itself by saving the Toa from a hostile flying Rahi by speeding up its life, killing it. The Toa did not notice another flying Rahi escape through the Makuta's portal into Karda Nui, with Vican riding it, heading for Destral.
When the Toa arrived in the Shadow Leech hive, they found no leeches, and just Mutran instead. Kopaka and Solek hung back to take on Mutran, while the others headed further into the hive, which seemed to be bigger on the inside than it was in the outside. They reached a dead-end, and when they turned around to see if was still behind them, they found that in his place was a gigantic monster. Without worrying about whether it was hostile or not, Tanma (and the others soon afterwards) jumped into battle.
They did not realize that this was an illusion put up by Mutran, and that this monster was actually Toa Ignika. Confused and enraged as to why the Toa were attacking him, he decided to use his Life powers to kill the Toa and their Matoran friends. But eventually the illusion faded and the Toa were able to disrupt Toa Ignika's attack.
Meanwhile, Mutran had attempted to tear Kopaka's mind to pieces, and Kopaka led him to believe he had succeeded, until eventually he turned the tides of the battle and froze Mutran in a blast of ice and snow. It was then that Antroz, Chirox, and Vamprah arrived and quickly defeated Kopaka and captured the heroes. The Toa were chained to a wall, and the Matoran were left in another chamber. Antroz warned the Toa that if they made one hostile move, he would send a mental message to Vamprah and Chirox who were with the Matoran to immediately kill them.
Pohatu collapsed the floor below the Makuta and used his to race to the chamber with the Matoran before Vamprah and Chirox killed them. He returned with the Matoran, and the Makuta not far behind. Pohatu shared his mask power with the others and the heroes sped around the chamber too fast to be seen and then escaped. Toa Ignika, using his life power, destroyed the organic stone cord holding the hive up and causing it to fall into the swamp.
Vican arrived on Destral before long, and delivered the message to Icarax, who was wearing the mask of Makuta and sitting in his throne. Though enraged that Antroz was giving him orders, Icarax decided to come, only to tell Antroz he was not to be ordered around.
By the time Icarax had arrived, the final battle had begun. The Makuta laid siege to the Matoran village...only to find that there were no Matoran there. The Toa Nuva and the Matoran were in the Makuta's base, searching for the third keystone.
When the Makuta went after them, a battle occurred. In the end, Mutran used the equivalent of a of . Icarax had earlier sent Antroz into the swamp, and Toa Ignika had made Icarax into a biomechanical being once more by de-evolving him. And after the Nova Blast, Chirox, Vamprah, and Icarax were nowhere to be found.
The Toa withstood the blast, and Mutran was forced to surrender. The Toa headed into the swamp to meet up with their friends. But elsewhere, Makuta Teridax's energy floated through an unknown location...a location that would "rock the Toa's universe" to discover.
It was a place heavily guarded, but Teridax easily crossed, having no body and being only a cloud of energy. He located his goal, a carving of a , and set about his final goal, to accomplish his .