After their Krana were removed, the Bohrok were reprogrammed to repair the damage that they had caused. The Toa were now stronger than ever before, now that they had been transformed into the Toa Nuva. The Bahrag were imprisoned and celebrations were in abundance. During the festivities, Hewkii found Pohatu's Nuva Symbol. At the same time, Tahu's Nuva Symbol had also appeared, and was inserted in a niche in Ta-Suva. Turaga Vakama then went into the Suva, explaining to Tahu about the Kanohi Vahi, the Legendary Mask of Time. He finally gave it to the Toa Nuva of Fire but told him to use it only in an emergency. After checking up on their villages, the Toa met again. After a brief talk, they had a show of their newfound powers, battling each other with their powers. After that, they talked about splitting up. Despite Gali's warnings of past events, everyone went their separate ways.
The Bohrok-Kal, six elite Bohrok, awoke. Their only mission was to free the Bahrag, but they did not know where or how to find them. Because of this, the Bohrok-Kal began to journey around the island searching for any possible areas where the Bahrag could have been imprisoned, and in the process, found out that they needed the Nuva Symbols to free the Bahrag. The symbols acted as a key to the cage. The theft of these symbols would take away the Toa Nuva's elemental powers.
That day, Lewa's Nuva Symbol appeared in Le-Suva. He then tried to show the Le-Matoran his flying powers, but plummeted due to the theft of his Nuva Symbol by Gahlok-Kal, and thus his elemental powers were lost. Fortunately, Kongu and Ka saved Lewa in freefall.
At Ko-Koro, Kopaka's Nuva Symbol also appeared. Matoro promised to guard it for him. Later, the Ice Toa was walking around Ko-Wahi, troubled by the separation of the Toa Nuva. Kopaka wondered if someone planned for this to happen. As he was walking over an ice bridge, his elemental powers were lost, as Nuhvok-Kal had stolen his Nuva Symbol. Despite Matoro's efforts at stopping the Bohrok-Kal, Nuhvok-Kal easily defeated him by increasing his gravity to the point that he could not stand up. Kopaka started to fall into the chasm below, but he managed to save himself by catching the side of the chasm with his tools. With the help of Turaga Nuju, who appeared on the scene, Kopaka was able to make it out of the chasm.
Jaller and Takua were journeying to the village of Ta-Koro. Along the way, Jaller heard a noise and readied his disk. However, the source of the noise was from Puku, who had followed Takua. The two Matoran and the Ussal continued on their way to village of fire. Once in Ta-Koro, Jaller and Takua went to report to Vakama about the Bohrok War. Upon leaving Vakama's hut, they saw one of the guards trapped in a field of electricity and a creature that looked like a Bohrok taking Tahu's Nuva Symbol from the Suva.
Jaller summoned an alarm and threw a bamboo disk at the Bohrok-Kal. Tahnok-Kal used its powers to trap Jaller and the disk in a field of lightning. Tahnok-Kal tried to get away, but Tahu was already at the gate. Tahnok-Kal fired electricity at the arch above the gate, making it collapse on Tahu, who tried to use his elemental powers to protect himself, which were already lost, letting Tahnok-Kal escape with the symbol.
At the same time, Onua's Nuva Symbol was stolen by Lehvak-Kal. Onepu tried to stop the Bohrok-Kal, but it sucked all the air out of the Suva, rendering Onepu powerless in stopping the theft. Onua went to tell the Turaga of the Nuva Symbol theft, and to regroup with the other Toa.
Meanwhile, Gali's Nuva Symbol was stolen by Tahnok-Kal. The Bohrok-Kal trapped the guards there by filling the Suva with electricity, pinning them to the wall.
Vakama explained to Tahu that the strange creatures were elite Bohrok with one mission-free the Bahrag. Then, Tahu, Takua, and Jaller went around the island to meet up with the other Toa. In Po-Wahi, they found Pohatu with several Mahi magnetized to him, a result of Gahlok-Kal's magnetic powers. The Toa Nuva met at their usual meeting spot near Kini-Nui and discussed the recent events, as well as their next course of action.
The Toa journeyed to Po-Wahi, where they traced some of the tracks. There, they had their first encounter with the Bohrok Kal. The Toa found out that they were searching for the Bahrag, but scoffed at this, believing the Bahrag to be long gone. The Bohrok-Kal, however, thought that the Toa knew where they were, and demanded of their knowledge. The Toa, not knowing of the queens' location, could not answer and so the Bohrok-Kal swarmed them with their powers. They couldn't withstand their powers, and fell unconscious. A little later, they awoke, groggy and disoriented. The Bohrok-Kal were long gone. The Toa vowed to retrieve their symbols, and stop the Bohrok Swarms from awaking once again, and cleansing the island of Mata Nui.
The Toa split up again. Kopaka, Lewa and Tahu went to search for the Bohrok Kal and delay them, while Gali, Pohatu and Onua went to investigate the Bohrok Nests to see if the Bahrag were still there. On their way, the Toa also began their quest for the Kanohi Nuva, which had appeared all over the island now that they had transformed into their new forms and lost all but their primary Kanohi, which had turned into a Kanohi Nuva. However, while they still succeeded in collecting most of their transformed masks, they were experiencing trouble with the Bohrok Kal.
At some point here, Kopaka went to search for the Hau Nuva, allowing Pohatu to join him. Later, they finally found it in an underground cave on Mount Ihu. Suddenly, there was a cave-in. Kopaka tried to use the Hau to protect both of them, but Pohatu was already buried by the rocks. After searching in the rubble for Pohatu, with no luck, Kopaka traveled to Po-Koro. He removed his Hau and gave it to the Matoran to remind them of Pohatu in the future. However, at that point, Pohatu arrived. It had turned out Pohatu was saved by the mask, and then dug his way out of the rubble.
Some time later, Onua and Whenua were going through a very long tunnel. At one point, they ran into a subterranean worm, but drove it off. Later, they encountered some Kofo-Jaga and had to back off. When the Kaukau Nuva was found, Onua and Whenua noticed that it was guarded by two Manas. Thinking quickly, Onua broke a portion of the cave wall, allowing some lava to flow in. The heat attracted the Kofo-Jaga, which drove off the Manas long enough for Onua to grab the mask and make a getaway with Whenua.
At one point, in Le-Wahi, a fire was started. Tahu tried to stop it, but remembered his powers were gone. He later met with Lewa, and they both tried to get two Kanohi Nuva, one for each of them. While going through Le-Wahi, the two Toa found uprooted trees scattered around an area, proof that Nuhvok-Kal had been there. Lewa wanted to ambush the Bohrok-Kal, and formulated a plan: Tahu would lure the Bohrok-Kal to a clearing, where the Le-Matoran would attack with various projectiles. The Nuhvok-Kal's gravity powers would be pushed for its limit, allowing for Lewa to steal the Krana-Kal within. Although most of this went according to plan, Lewa was struck down by Nuhvok-Kal's gravity powers as he tried to steal the Krana-Kal. Tahu saved Lewa, and Nuhvok-Kal took advantage of the distraction to slip away. The two Toa resumed their search for the masks and eventually found them.
While this happened, Hahli then rowed to Nokama and told her that Gali's powers were gone. Nokama thought that the Toa would need all the help they could get. She started Gali off by trapping Gali in the underwater cave where she had hidden a Kakama Nuva and where she had carved the Toa Metru. Gali later noticed the carving, and thought one of them looked sort of like Nokama. Soon after that, she was attacked by a tentacled Rahi. While fleeing, she found the Kakama, which she put on and activated it. She directed herself at the cave's exit, and her molecules moved so fast that she went right through the wall of the cave. When she met with Nokama, she asked about her past as a Toa. Nokama laughed and said she was a Turaga, not a Toa.
Gali later summoned Tahu and Kopaka. They went to the Place of Shadow to find three Kanohi Nuva. Along the way, they face illusions and dangers. Just when they are moments away from reaching the Kanohi, the ground disappears, and they fell into a cave. However, the three Toa managed to obtain the three masks. They soon discovered the other Toa and Vakama were trapped there, too. Vakama remembered what was trapped there, when the Rahi Nui attacked. Vakama then used the monster's memory to make it agitated. Taking advantage of the beast's lack of brains, Vakama was able to make the Rahi Nui lodge its horns into the cavern wall.
Later, Lewa tried to sneak up on Kohrak-Kal, but was blasted by its sound power. In addition, Tahu led some Tahnok against Nuhvok-Kal. The Bohrok-Kal simply used its Gravity power to keep them in orbit. Then it slammed Tahu into the ground.
Elsewhere, Kopaka, Gali, and Lewa merged into Wairuha Nuva in an attempt to defeat Lehvak-Kal, but the Bohrok-Kal formed its own Kaita with Kohrak-Kal and Gahlok-Kal and defeated the Toa Kaita. Meanwhile, Onua and Pohatu plotted against Tahnok-Kal with a plan. They reflected its lightning bolts at a tree behind it, and it fell on the Bohrok-Kal. They removed its Krana-Kal, but it laughed told them telepathically that the Bahrag had been found. Turaga Nokama arrived on the scene and confirmed this to the two Toa. Some Boxors were able to remove the Krana-Kal from another Bohrok-Kal and learned the same thing. This Bohrok-Kal was able to escape when a Bohrok Va supplied it with another Krana-Kal. As the two Toa turned their attention back to Tahnok-Kal, they realized it had ran off. A Bohrok Va had given another Krana-Kal to this Bohrok-Kal.
Elsewhere, Tahu attempted to defeat Pahrak-Kal on his own. He almost lost to the Kal's Plasma powers, but Jaller and several guards from Ta-Koro saved him. Jaller was able to remove the Krana-Kal from Pahrak-Kal, but then a Gahlok Va came along and placed another one in. The Toa regrouped, hastily followed the tracks that the Kal made, and soon ended up in a very familiar place: the entrance to the Bahrag's lair. It had been blasted open by Pahrak-Kal's powers. The Toa returned to the familiar but destroyed Bahrag cave. Rubble lay everywhere, but a hole was in the ground. Lewa then descended to see what was happening.
The Exo-Toa suits were running on automatic and fighting the Bohrok-Kal, but were being destroyed by the Bohrok-Kal's powers. Before them was the Nuva Cube, with markings of the Nuva Symbols upon them. Behind that was the Protodermis Prison, which encased the Bahrag. Lewa Nuva levitated back up and warned the Toa about what was happening, and they all rushed into the lair. The Bahrag laughed and cried out that the Toa Nuva were too late.
The Bohrok-Kal began to lift the Nuva Symbols into the cube. The Toa began to attack, but they ended up hitting an invisible force field. The Krana-Kal had turned a sudden silver, protecting them from all physical harm in their last moments before they freed the Bahrag. The symbols were almost placed. In desperation, Tahu Nuva called for the Kanohi Vahi, the Great Mask of Time and used all his strength to delay the Bohrok-Kal. However, the strain was starting to be too much for him. They had only a minute or two before the Bohrok-Kal woke from the time freeze and placed the Nuva Symbols into the cube. However, it bought them enough time for Gali to know what to do. Using all of her willpower, and joining forces with the other Toa, they connected to the Symbols mentally and pushed their power into the symbols and into the Bohrok-Kal. Instantly, the Bohrok-Kal felt immense power going through them and stopped what they were doing, believing that they did not need the Bahrag's or the Bohrok's help in cleansing the island.
However, the power was too much for the Bohrok-Kal. Tahnok-Kal's electricity overloaded and he became trapped in his own electrical field. Lehvak-Kal was pushed up out of the mountain and into the sky from a large blast of Air. Kohrak-Kal was trapped in an immense field of energy and sonic sounds that disintegrated him. Gahlok-Kal's Magnetism smothered it in pieces of the destroyed Exo-Toa. Pahrak-Kal melted beneath the ground below him into Plasma. Nuhvok-Kal's own Gravity powers imploded it into a miniature black hole. As the Bohrok-Kal's energies began to die down, they fell, one by one, and only the Krana-Kal survived.
The Toa Nuva retrieved their Symbols, exhausted, as the Bahrag Cage's clear shell of Protodermis blanked out the view of the twin Queens and their raging screeches. The Toa Nuva had succeeded, stopped the Bohrok-Kal and retrieved their elemental powers. Kopaka Nuva led the Toa Nuva out by using his replenished elemental powers to create a staircase made of ice. A temporary period of peace followed.
During this peace, the Turaga held a Naming Day celebration in honor of the Matoran who contributed to defending Mata Nui from the Rahi and Bohrok. After the celebration was over, Takua re-named Puku as 'Pewku'. The Turaga also upgraded the Matoran's bodies, using their knowledge of rebuilding. Jaller and Takua were the first to be changed, and they showed the other Matoran.
One night a massive storm ravaged Ga-Koro and awoke Hahli who was having a strange dream. After repairing her house she talked to her boss, Amaya and repaired the bridge going to the main city. She heard the news about Nokama coming to announce the players the Kolhii Tournament being help in celebration of the Bohrok-Kal's defeat. Hahli continued her day-to-day work, Nokama then arrived and picked Macku and her to be Ga-Koro's Kolhii Championships. The village was shocked, having expected Kotu to be chosen instead. Hahli went to Nokama and Nokama told her that she saw Hahli's face in the water, and the Ga-Matoran found the key to Nixie's hut. Nixie explained her Toa Formula, but something was temporarily wrong with the math. Talking to other Ga-Matoran, Hahli was given three Charms by Shasa, Kai, and Marka representing Unity, the Kolhii Skill of Speed, and the Principle of Purity. Pelagia then took Hahli in a Boat to coordinates C9 in the ocean where she uses Air Bladders from Okoth to race a Takea, improving her Speed. In the match against Onu-Koro's Onepu and Taipu, this helped Hahli and Macku prevail.
The Onu-Matoran graciously invited Hahli and Macku to their village, and meets Whenua and goes into the Marn Tunnels, meeting Dosne, the chief miner. She helped some of the miners complete tasks, including diving in the flooded Great Mine to retrieve machinery. She also met with Nuparu, who would giver her fitness checks, and Taipu. Taipu trained her in Stamina by carrying heavy rocks, and Hahli got Stamina's charm from him as well. After retrieving a Sluice for Azibo, Hahli is given Prosperity's charm. Macku gets her to head to Ko-Koro where they have to face Matoro and Kopeke. Upon arriving she talked to Nuju and other scholars at the Wall of Prophecy, and got Destiny's charm from Jaatikko and Peace's from Toudo. To learn Willpower she sought out Kantai in the The Drifts, and found the charm, and balanced on a precarious position to gain Willpower. In the Kolhii match, she then used her Stamina and Willpower to secure victory.
Hahli then toured Le-Koro before her next match there, and talked to her opponent Kongu, finding the Faith charm in his hut. After exploring the village, she talks to Makani and Sanso the musicians about Le-Koro's values. Getting Bamboo Disks, Hahli then trained in Accuracy at a Le-Koro range, and found its charm there. Using the Le-Matoran Accuracy principle against them, Hahli defeats Kongu and Tamaru. Next the Ga-Matoran went to Po-Koro, and met Hafu and Kamen repairing the Path of Prophecies. She then met Macku's good friend Hewkii, and discovered Creation's Charm, and met the Mahi herder Golyo. He taught her about Strategy, and Hahli found the charm while Mahi herding. In Ga-Koro's biggest upset yet, Macku and Hahli defeat Hewkii and Hafu. Po-Koro reacts with anger and shock at getting defeated at their own game.
The last team to face is the other good team from Ta-Koro, Takua and Jaller. Takua wished Hahli luck in the game ahead after she arrived in the village, and she then she was greeted by Vakama. After talking to Kapura, Hahli met Jaller. Jaller confessed he wanted to beat her, but still sent her to see Keahi to train in Strength. Keahi let Hahli train in Strength, throwing Kolhii Balls in the lava lake surrounding Ta-Koro. This is key, as Hahli manages to defeat Jaller and Takua. Ga-Koro has emerged as the sole undefeated team, setting up a three-way duel with Po-Koro and Ta-Koro in the Championship.
The Turaga later debated whether the Toa Nuva should know about Metru Nui. To prove if the Toa were worthy to know or not, they quickly related the tales of how they got the Kanohi Nuva. After sharing their tales, the Turaga realized the potential loss that could be had if they continued shielding the Toa from their secrets. Jaller then came in, asking if they knew where Takua was as the Championship was about to start. After learning they did not, he left. The Turaga then agreed that after the Kolhii Tournament they would tell the Toa.
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