The Battle of Bara Magna was a massive battle fought between the gigantic robotic forms of Mata Nui (Prototype Robot) and Makuta Teridax (Great Spirit Robot) and their respective ground-based allies that determined the fate of the Matoran Universe and Spherus Magna.
- Stop Teridax from conquering or destroying Bara Magna and any worlds beyond it.
- Save all the inhabitants of the Great Spirit Robot and prevent them from being harmed.
- Reform Spherus Magna using the powers of the Prototype Robot.
- Stop Teridax's forces of Heat-Vision Rahkshi, Skakdi and Skrall
- Save Mata Nui from Teridax and his more formidable robot body.
- Gather the Golden Armor so Tahu can use it to gain the upper hand in the battle and destroy most of Teridax's ground forces.
- Defeat Mata Nui once and for all.
- Either conquer or destroy Bara Magna and any worlds beyond it.
- Defeat the Glatorian, Agori, and Toa
- Assist Teridax in conquering the planet.
- Stop Tahu from gathering the Golden Armor to defeat them all.
- Defeat the Glatorian as revenge for their own defeat in the Battle of Roxtus.
Mata Nui asked Raanu to evacuate the Agori from the United Village, so he could use the Prototype Robot that the shelters were based in. He took control of the robot and began to draw its moons, Bota Magna and Aqua Magna, toward Bara Magna to reform the shattered planet of Spherus Magna. Teridax arrived during this process, having taken off from Aqua Magna to find Mata Nui. He taunted Mata Nui, who informed Teridax of their destiny to reform the planet.
Teridax shot a blast of energy past Mata Nui's face that hit one of the Black Spike Mountains, incinerating it.
Teridax offered Mata Nui the chance to join him in his efforts to gain control of the universe. Mata Nui refused, saying he had to complete his destiny, only to be shot in the shoulder by one of Teridax's lasers.
Mata Nui tried to explain to Teridax the Great Beings intent for him, and that he was trying to do the people of Bara Magna justice. Teridax found where the Agori and Glatorian were hiding, and used his gravity energy to raise the mountain in the air, exposing the people of Bara Magna. Mata Nui then fired at Teridax, but the mountain began to fall on the Agori and Glatorian. Mata Nui blasted the mountain to dust, and told the Agori to run, and they began to.
As Teridax and Mata Nui began to fight, the Glatorian grew worried for Mata Nui, but Gresh came up with a plan to try and stop Teridax. All the Glatorian, divided into squads led by Kiina and Ackar, charged the giant robot and fired their Thornax at the robot's foot, but they did no damage. Gresh had split off from the rest of the group to create an entrance through which he and the Glatorian could enter the Matoran Universe and destroy the robot from the inside.
Mata Nui blasted Teridax but soon realized that the Prototype Robot was breaking down. Teridax reminded him of the thousands of beings inside him, and that if Mata Nui fought Teridax too much, he might kill them, as the last blast created a quake inside the Matoran Universe. Teridax noticed the Glatorian congregated at his feet, but decided not to fire on them, instead planning to release Rahkshi and Skakdi to combat them. Meanwhile, Gresh had found a hatch that led to the Southern Islands of the Matoran Universe that was located at the base of one of the robot's feet, and decided to open it. Before Gresh could fire a shot, an army of Rahkshi emerged from the hatch along with Nektann and a troop of Skakdi loyal to Teridax. The invaders then began to attack the Glatorian, catching them by surprise.
As Kiina was about to be defeated by a Rahkshi, Ackar cut its head off, and discovered that the Rahkshi were simply robots operated by slugs. As Gresh planned to enter the Matoran Universe, Tahu emerged from the hatch, followed by Takanuva, who changed his armor color for camouflage. Mistaking the two for foes, Gresh attacked the Toa with a tornado, angering Takanuva, who blinded him with light. As Takanuva prepared to finish Gresh off, the Glatorian cried out he was an enemy of Makuta and thought that they were part of his forces. Tahu then helped him up and told him to stay on Bara Magna and help them defeat the Rahkshi and Skakdi. Gresh agreed and went to battle Teridax's forces with the Toa. The three were followed by a group of Toa that emerged from the hatch to aid in the battle.
On the ground, the Rahkshi and Skakdi were attacking the Glatorian, managing to kill some. Teridax showed Mata Nui this and blasted him, declaring the planet as his. Elsewhere, up on a rise overlooking the scene, the elite Skrall warrior Stronius, accompanied by a large group of Skrall, observed the battle and announced his plan to attack the Glatorian.
Tahu began to advance onto Bara Magna, but was drawn into a vision of a lava plain where the Ignika confronted him, and devolved him back to a Toa Mata. Tahu was angered by this, but the Ignika told him of the Golden Armor and the message sent by Tren Krom. The mask dispelled the illusion, and created the Golden Armor in front of Tahu and Takanuva. Teridax noticed this and fired at the armor, scattering it across the desert. A piece of the Golden Armor landed at the feet of Gresh after he had used a controlled cyclone to send a half dozen Rahkshi flying. He picked it up, and saw three Skrall with another armor piece. As he pondered over the piece of armor, a Skakdi warrior with a twin-bladed axe came charging toward him. Elsewhere, Nektann had defeated a Glatorian and looked around to see a Rahkshi losing in battle to a native warrior and two villagers. As he approached to help the Rahkshi he batted aside an Agori who got in his away and noticed a piece of golden armor buried in the sand. He picked it up and continued.
The other Toa Nuva began to arrive, with Gali, and Pohatu decimating half a legion of Skakdi. Far above the battle, Mata Nui and Makuta were lighting up the skys, expending all of their energy in their personal battle. Mata Nui fired a bolt of pure energy at Teridax's chest in the same spot as before, causing failures in the Matoran Universe robot's systems. Teridax taunted Mata Nui, saying his new followers did not stand a chance against his forces. The former Great Spirit replied to Teridax that the people of Bara Magna would not surrender, resulting in Teridax resolving to destroy the planet with a blast of gravitic energy.
Meanwhile, down on the surface of Bara Magna, two Rahkshi of Heat Vision with an armor piece advanced on Takanuva. In an effort to defend himself, Takanuva created a hologram of himself and willed the hologram to run in between the Rahkshi. They both fired their heat vision at it, unintentionally hitting each other and allowing Takanuva to take the armor piece. Meanwhile, Tahu was fighting Nektann for the shield, with the Skakdi warlord taunting him. Tahu explained that he was wiser now and would not fall for the tricks he used to be duped by. Nektann picked him up, grabbing him by the neck, but Tahu began to melt his enemy's armor, knocked the warlord out and took the shield. Just as Teridax was about to destroy the planet with his gravitic blast, Mata Nui redirected the blast into the sky, where it hit Aqua Magna and Bota Magna and began to draw the two moons to Bara Magna. Mata Nui saw them coming and began to force Teridax to the north.
Gresh created a tornado around the Skrall, took their armor piece and gave his two to Takanuva and Tahu. An entire legion of Rahkshi was advancing rapidly on the three, and Tahu quickly put on the Golden Armor and used it, causing bolts of energy to be released, destroying the Kraata inside the Rahkshi on the battlefield and disabling them. The sudden death of thousands of his Rahkshi was felt by Teridax, who staggered as Mata Nui, with a last desperate effort, shoved him into the path of a fragment of Aqua Magna that split off from the moon. It struck Teridax in the back of the head, crushing the Core Processor and killing the Makuta. The tyrant fell and, with both the Rahkshi and Teridax defeated, the Skakdi and Skrall surrendered to the Glatorian and the Toa.
With the core systems of the Matoran Universe destroyed, the Energy Storms stopped in Karda Nui. Most of the Matoran Universe's inhabitants left the universe. The Aqua and Bota Magna moons hit Bara Magna, reforming the planet of Spherus Magna after 100,000 years, during which it had been fragmented. Mata Nui drew upon the Mask of Life and the Prototype Robot's power to bring life to Bara Magna, resulting in grasses, trees, and flowers growing in the desert. The robot then fell apart, too stressed by the recent fight to endure the exertion. The Toa and Glatorian rushed to the site, finding the Mask of Life intact, and to their surprise, that Mata Nui's spirit had been drawn back inside it. Tahu suggested Mata Nui utilize the Ignika to create a new body, but Mata Nui decided to stay in the mask and not interfere with the new life that the Toa, Glatorian, Agori, and Matoran now have. Glatorian Kiina cradled the mask, asking if Mata Nui was gone. Tahu assured her he was not gone, and led the people of Spherus Magna to start a new life.