After the defeat of Teridax, which signaled the end of the Dark Time, Takua emerged from under the remains of Teridax's "vortex" form, after witnessing the Toa Mata's battle with him. At the other end of the room, a large, circular door, with the same sign on it as Takua had once seen in a dream, opened. Takua entered.
A massive hive-like structure stood before Takua, and as he approached, red eyes glinted. A pod opened and the creature emerged. Takua attempted to flee as more pods opened. He discovered a golden sphere, but there was a piece missing, which Takua recognized. He searched in his pack for the object he was thinking of, tossing away everything he had to find it. Having been successful in his search, he slammed the Po-Koro Chisel into the sphere, and was soon surrounded by a bubble of energy. The bubble then swiftly transported Takua up to the top of the chamber and through a tunnel, tossing him out through the Bohrok Nest Portal, onto the Ta-Wahi Beach.
Turaga Vakama was waiting there, and congratulated him for proving him wrong, thinking Takua had been killed, as well as the Ta-Matoran, who feared that he would bring bad luck. Then, as fireworks went off, Takua and Vakama walked back to Ta-Koro together, and the Red Star glowed brighter than ever.[MNOG, Ch. 9]
At Kini-Nui, the Toa Mata were discussing their victory. While walking, they discovered Kapura. The Toa used the Kakama power of their Golden Kanohi, to rush to Ta-Koro, (while carrying Kapura) to see what had happened. The Pahrak and Kohrak were still attacking Ta-Wahi. However, they were not attacking the Matoran, just the land, and even ignored the Toa, unless the Toa got in the Bohrok's way. Lewa attempted to create a cyclone, but one blast from a Kohrak froze him in mid-attack, then sent him crashing to the ground, too heavy to stay in the air. Tahu levitated over using the Miru power of his Golden Kanohi, and dispersed the Kohrak as he melted the ice around Lewa. The Pahrak chose this time to create an avalanche directed at Pohatu. Before the stones could impact Pohatu, Onua used the Kakama power of his Golden Kanohi to get him out of the way in time. Tahu then ordered Gali and Lewa to combine their powers, in order to create an immense cyclone with blue and green lightning. With such might of storm before them, the Bohrok fled. All but one Pahrak, who lay on the ground with its head piece open and its Krana showing.
Vakama stood high above, and told the Toa the story of the Bohrok. He explained that they needed to collect all eight types of Krana from the six types of Bohrok in hopes of defeating their invasion. The Toa decided to split up and search their own individual region.[C4]
Tahnok were beginning a siege in Po-Koro. Turaga Onewa and the Po-Matoran had no way to escape, for there was only one way out, through the Path of Prophecies, where the Tahnok were approaching from. The Po-Koro Guard planned an attack on the swarm, but in the last moments, when Tahnok were very near, Hafu knocked down some of his Matoran face statues at the gates. This blocked the way to Po-Koro, but trapped Hafu outside.[BOA, Ep. 1] The Tahnok were now right in front of him, preparing to shoot a Krana, but just in time, Pohatu arrived and saved Hafu. Pohatu then used his noble Kanohi Komau to make Hewkii kick a Kolhii ball down onto a rock which he and Hafu were on. This caused the stone to act as a catapult, throwing Pohatu and Hafu back into Po-Koro.[BOA, Ep. 2] Po-Koro was later attacked by Lehvak and Pahrak. Pohatu defeated them, gaining a few Krana.[citation needed: BC2?] Despite Pohatu's victory, Po-Koro had to be evacuated, for the Bohrok had caused much damage there.[BOA, Ep. 5]
Onu-Koro was, after a Nuhvok attack, attacked again by Gahlok, who tried to flood the caves. As a result, Onu-Koro was being evacuated, its residents moving into a different section of Onu-Wahi. Onepu and Taipu stayed by the exit which the Onu-Matoran were fleeing through, sending others out. Taipu held a huge rock above him, which they planned to use to block the entrance from Onu-Koro to the area, where Turaga Whenua and the Onu-Matoran would be, after everyone had fled the Koro. Nuparu was the last one attempting to evacuate, but just as he was at the exit, the water rushed into Onu-Koro. Nuparu, however, got inside at the last moment, trapping the three of them inside a cavern. With Nuparu's Lightstone, the cave was illuminated, however the Matoran were startled. A disabled Gahlok with no Krana was found. Onepu and Taipu began clearing some fallen rocks, in an attempt to free themselves, while Nuparu tinkered with Gahlok's parts. Taipu and Onepu started to help, and soon the invention was finished. Nuparu used this to defeat the Gahlok in Onu-Koro, naming it the Boxor.[BOA, Ep. 3] He then started traveling around Mata Nui with Takua and his new Boxors, along with a few drivers to help other villages.[WoH]
While the other Toa were searching alone, Pohatu and Gali had teamed up, and formulated a plan. One week after the Bohrok awoke, the Toa all pitched in to help out their plot. In the middle of Po-Wahi, Onua dug a tunnel from Tiro Canyon to the sea, just before leaving for Le-Koro to check on Lewa, as the Toa had not heard word from him since they parted. Kopaka plugged the tunnel entrance solid with ice, so the water would not break through, yet. Just as Tahnok were rapidly moving through the canyon, Pohatu kicked a stone at the ice dam. With the plug shattered, the water surged in and soon flooded the Tahnok. Gali then dove in after the Tahnok, who had heated the water to a high temperature, managing to retrieve four Krana. After an attempt by three Tahnok to crush Gali with a slab of the canyon wall, she resurfaced, and with Pohatu, they fled before the Tahnok could climb out. The two Toa ran all the way to the edge of Po-Wahi, only to be confronted by Gahlok.[C5]
At the same time, Kopaka had pursued a Tahnok Va into a cave which was filled with many more. Kopaka located Tahu in Ta-Wahi, giving a motivational speech to a group of Ta-Matoran.[C5] Kopaka told Tahu of the cave and they traveled there. Upon viewing the cave, the two Toa came to the realization that the Bohrok were not creatures from any other land, as they had thought, but that they came from within Mata Nui itself. Tahu started to charge in, in an attempt to bring an end to the Bohrok, but Kopaka stopped him, reminding Tahu that the Krana were the key to defeating the Bohrok.[BC2]
Meanwhile, Onua found Lewa in Le-Wahi. Lewa struck him with an Air attack and told him to flee, as the Krana was controlling his body. But Onua stayed, telling Lewa that he was stronger than the Krana, and that he should prove himself worthy of being a Toa. Lewa tore off the Krana, and Onua gave him his mask, explaining that he retrieved it from some Lehvak Va earlier. Lehvak then came charging at the two Toa, but Onua had brought a group of Boxors with him, which quickly surrounded the Bohrok. Lewa told Onua that he could hear the voices of the swarm while under the Krana's control, and that the Toa needed to act then, or there would not be anything left of Mata Nui.[C6]
In Le-Wahi, a small group of Matoran had a camp. Takua, Nuparu, and a few other Onu-Matoran Boxors were there, planning to free the Le-Matoran, most of whom were still under the influence of Krana. Kongu and Tamaru, the only Le-Matoran who had escaped the Bohrok, entered the camp and were greeted by Takua and Nuparu. Kongu and Tamaru explained that they were the only Le-Matoran who survived, and that Lewa was also under the power of a Krana. Takua however knew that Onua had helped to free Lewa, and informed this to the two Matoran who were overjoyed to hear the news. Together, the four Matoran contemplated a plan to defeat the group of Nuhvok, which were now residing in Le-Wahi, and free the Krana-wearing Le-Matoran.
In the morning, the plan was set into motion. Kongu and Tamaru located the Nuhvok swarm and harassed them, causing the Bohrok to pursue them as they swiftly fled through the trees of Le-Wahi. The two Le-Matoran lead the Bohrok to a clearing, where Turaga Matau and the Le-Matoran ambushed them, along with the Nuhvok which had been chasing them. Kongu and Tamaru were surrounded and the Nuhvok prepared to launch their Krana at the two Le-Matoran. Suddenly, Boxors erupted from underground, engaging the Bohrok and Krana-wearing Le-Matoran, trapping them. Takua and Nuparu removed Turaga Matau's Krana and the Le-Matoran's as well. Le-Koro was taken back after the struggle.[BOA, Ep. 4]
While in the canyon, Gali and Pohatu encountered a group of Tahnok destroying the area. Angered, Pohatu created a wall of stone to impede their progress, while Gali used moisture in the surrounding area to summon a flood to sweep them away. The two Toa then regrouped with their allies, and Kopaka informed them of his find. Telling them of the Bohrok Nest, the six Toa agreed to descend into the tunnel and end the threat of the Bohrok once and for all.[C6]
Into the Nest
Walking down into the tunnels, Tahu spoke to Onua about his suspicions. Believing that Lewa was still influenced by the power of the Krana, Tahu told Onua to keep an eye on him. Onua, however, shrugged this comment off, saying that, in the end Lewa was strong enough to overcome the power. While Tahu and Onua quarreled, Pohatu noted aloud how the tunnel in which they traveled in had incredibly smooth walls. Gali, shocked by this, spoke more with Pohatu, and the two became very uneasy. Meanwhile, Lewa spoke to Kopaka, worried that the swarm influenced him still.[BC2]
Before Kopaka could finish answering, the Toa Mata encountered a hole in the path. Tahu, using the Miru, traveled down, finding a massive nest. As he hoped that they would not awaken, he was proven wrong, as they awoke right before his eyes. The pathway above blocked, Tahu was trapped down below, while the other Toa were trapped above. To add to their worries, Kopaka noticed a stream of molten lava bearing down on them. While Tahu attempted to escape the Tahnok bearing down on him, Kopaka used his powers over ice to keep the lava at bay. Lewa, seeing Pohatu and Onua working desperately at destroying the floor barring their path, realized that the wall must be an illusion. Thrusting his axe through it to show them, the Toa were astounded. Traveling through, the six Toa felt the ground beneath them growing hot. As Kopaka quickly urged them to get down, the wall was blasted through.[C6]
As Tahu entered the room, he related to the others what had happened to them. As he finished, the floor gave away beneath them, leading to a massive chamber. Seeing the niches in the floor, the Toa began to place the Krana into them. When all the Krana were placed, the chamber began shaking, opening six passageways. Each of the Toa entered their own passageway, and found a massive suit of armor waiting for them, Exo-Toa. Donning it, the Toa pressed into the next chamber, and found the monstrous Bahrag waiting for them. Firing his blaster, Tahu injured one of the creatures, and together, the Toa drove the two creatures into the first chamber. Before they could strike again, a shield formed around the Bahrag, protecting them. Informing the Toa, they told them of how driving them together only increased their power, and unwittingly, they had actually helped the Bahrag.[C7]
Continuing to fight, the Toa struck back against the Bahrag, fighting a losing battle. While four of the Toa were battered by the Bahrag's control over elements, Pohatu and Onua fought thin air, duped by the Bahrag's illusions. Seeing Tahu close to unconsciousness, Gali shouted for Pohatu and Onua, breaking the illusions, and shocked that they were duped, struck back. Soon after, the Toa shed their armor, as Tahu realized that it hindered their elemental abilities. Combining their powers, the Toa Mata sealed the Bahrag in a cage of Protodermis, disabling their connection to the swarm.[C8]
Siege of Ga-Koro
Meanwhile, on the surface of Mata Nui, Takua and Jaller traveled to Ga-Koro to speak to Turaga Nokama. Once there, Jaller told Nokama that Vakama had requested for he and his guard to come, in order to help protect the village. Takua had arrived with tidings of the creation of the Boxor, with which some riders came as well. Nokama, although pleased with this, told the Matoran that Pahrak were already at their gates, and close to attacking. At that moment, Kotu, Nokama's left hand, interrupted the meeting, telling her that something strange was going on outside her hut. The Ga-Matoran watched in wonder as boats traveled to their village, with Turaga Onewa at the head. Docking, Onewa told Nokama how they had traveled to Ga-Koro to seek shelter from the Bohrok, as Po-Koro was currently under siege from swarms of Tahnok and other Bohrok. Observing the Pahrak at the gates, Onewa noted how they had made a bad choice in arriving at the village at the current moment. As he finished, the Pahrak began invading the village.
In an effort to help, Macku, Hahli, and Kotu began attempting to destroy the causeway which led to the village, in efforts of stopping the Bohrok cold. Before they could finish, the Pahrak struck the village gates, sending boulders flying towards the Matoran. As one bore down upon Macku, Hewkii jumped in the way, and hit the boulder away with a Ga-Matoran fishing net. His actions would later inspire a reform of Kolhii, which would be played after the Bohrok War.
Saved, the Ga-Matoran relaxed with the Po-Matoran in the evening. While Macku spoke to Hewkii in thanks for saving her, Jaller, Takua, and Hahli walked in, saying how the Pahrak would find a way to get past this. Later in the night, the Pahrak struck the Kaukau waterfall, forming a bridge to the Koro.[BOA, Ep. 5] The Pahrak stormed the village, destroying much of it. Armed, Matoran in Boxors went forward, attacking. The Pahrak simply overturned the bridge, sending both machine and pilot into the water. While several Ga-Matoran saved the pilots, the Pahrak were again trapped from the village. At that moment, three Pahrak Va arrived on the scene, and gave the Pahrak Krana Vu. Enabled to fly, the Pahrak flew onto where the Matoran were, prepared to defeat them once and for all.
Takua and Jaller, camping outside the village, were shocked by what was unfolding. Unable to assist from their position, the two Matoran were stranded for a time before Takua, struck an idea and told Jaller to pull back a bamboo staff. On top of it, Takua told Jaller to let go, launching the Chronicler toward the Matoran. Facing the Pahrak, Takua prepared to defend himself with the other Matoran.[BOA, Ep. 6] At that moment, the Toa Suva glowed with light, and a symbol spun on top of it. From the Suva fired bolts of light, disabling the Bohrok. Nokama, awed, told the Matoran that the Toa had succeeded, and that the threat of the swarm was over.[BOA, Ep. 7]
Victorious, the Toa felt a rumbling beneath their feet. As the floor gave away, the Toa Mata were thrust into tubes of Energized Protodermis. Onu-Matoran miners had been mining a form of this material for ages, but, no one knew how a being would react to the substance. The Toa experienced many feelings inside the canisters, those of heat, cold, and many more. When the experience ended, the Toa rose up, transformed by the Energized Protodermis. Given new armor and new tools, the Toa took a moment to examine their armor, right as boulders of earth rained down upon them. Activating his mask, Tahu used the Hau Nuva, protecting all of the new Toa Nuva. Surprised, Tahu noted the new abilities of his mask. He then instructed Lewa and Pohatu to use their masks to get them out of the chamber, and with the combined powers of speed and flight, the Toa Nuva escaped.[C8]
In Ga-Koro, the Matoran busied themselves with repairing the land. While many Matoran labored over the Kaukau Waterfall, others harvested all the Krana and put them into a massive pit. A Bohrok then thrust a boulder on top, preventing the Krana from ever escaping. While Takua, Jaller, and Hewkii observed, they noted the new form of Kolhii that had been brought about. While Hewkii was dragged away by Macku for his swimming lessons, Jaller went with Hahli, to enjoy some days in the sun. Takua then looked to the ocean, thankful for the end of the war, but unaware of the threat arising yet again.[BOA, Ep. 7]
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