After being given new armor and weapons by Artakha, the Toa Nuva arrived at Karda Nui, the core of the universe. There, they came to face the Makuta who were trying to turn the population of Av-Matoran – Matoran of Light – into Shadow Matoran. The Toa Nuva were helped by the arrival of Takanuva, now able to control Light and Shadow because of a shadow leech attack, and Toa Ignika, who is the Mask of Life itself. The Kanohi Ignika had made a body for itself because it wished to see what it was like to be a living being. With their combined forces, they reached a structure in the center of Karda Nui called the Codrex, where Toa Ignika had to sacrifice his new body to awaken Mata Nui. Takanuva, with the help of the remaining uncorrupted Av-Matoran, returned the Shadow Matoran to their previous states. Shortly afterwards, the Toa escaped the core before the energy storm caused by Mata Nui's awakening could destroy them. The Makuta, however, failed to escape, and were all killed. Back in Metru Nui, Mata Nui's awakening was celebrated, but celebration was cut short when it was revealed that Teridax had taken over the body of Mata Nui, revealed to be the universe of the Matoran. Trapping the spirit of Mata Nui in the Mask of Life, he sent it flying into space so that the former Great Spirit cannot interfere with his control over the universe.
The Bionicle story continues after Mata Nui was banished from his body by Makuta Teridax, onto a planet called Bara Magna. With the exception of a few wildlife species, Bara Magna is a barren desert planet which only supports few resources, so each tribe on the planet has a few warriors, called Glatorian, to battle for them. These resources, such as food and water, are distributed accordingly. The villagers of this world are known as Agori. The Agori together make up six different tribes, each affiliated with a region. After the Mask of Life lands on Bara Magna, it creates a body for Mata Nui to use. Mata Nui then teams up with a few Glatorian to defeat the combined forces of the Skrall and Bone Hunters, two major threats to the villages, and look for a way to return to his body. With the help of his new Glatorian and Agori friends he exposes a traitor known as Metus and defeats the Skrall and Bone Hunters. He helps the villages of the world to unite, taking all of the giant pieces of robot and linking them into a large prototype robotic body, a body like the one the Matoran Universe resides in.
After defeating the Skrall and seeing the rest of the villages unite, Mata Nui stands against the challenge of taking back his old body from Teridax. He learns that he was created by the Great Beings on the planet of Spherus Magna, which is now divided into a jungle moon (Bota Magna), an ocean moon (Aqua Magna), and the remaining desert planet (Bara Magna), as the result of the Core War. Mata Nui also learns that before he was built, there was a previous robot, which the Agori use as their home. An Agori of Tesara named Tarduk helps Mata Nui by showing him an ancient power source that could power up the old robot.
In this final journey, two heroes return to finish the fight: Tahu, returned to his original form to wear the powerful Golden Armor, and Takanuva. They are aided by Gresh. They fight off the Skakdi Warlord, Nektann to defeat Makuta, and his army; hordes of Rahkshi, armed with heat vision; and Skrall.
The story continues as the forces of both the Matoran Universe and Glatorian face the oncoming onslaught of Skakdi, Rahkshi, and Skrall. The golden armour, scattered by Makuta's blast is collected by Tahu, Gresh, and Takanuva from the many enemies. Tahu defeats Skakdi warlord Nektann, and then dons the armour, which incinerates every Rahkshi Kraata on Bara Magna.
Teridax claims that he will destroy Bara Magna with gravitic energy, until Mata Nui forces his arm upwards, causing Teridax to send the energy wave to the moons above. Mata Nui pushes Teridax back into one of the onrushing moons, the green moon of Bota Magna, whose impact destroys his core processor, which kills Teridax. Mata Nui then mourns the brother that he could have had, in his mind.
The finale concludes when Mata Nui uses his strength, and the power of the Mask of Life, to bring Spherus Magna together once more, to heal those who were mutated by Pit Mutagen, to bring life back to the planet, and to reconstruct destroyed geographical features. The strain causes his power core to dissipate, destroying the prototype robot. When the Glatorian and Toa discover the Ignika unscathed in the location where Mata Nui was, Mata Nui speaks to them from within the Mask of Life. He tells them that the future is their own and theirs to build. He then remains dormant in the Ignika. The Agori, Matoran, Toa, Glatorian and all others begin a new life on Spherus Magna.
The Bionicle toyline drew to a close in late 2009, after the 2010 sets were finalized for release, and was replaced in the summer of 2010 by Hero Factory, a Lego theme that´s compatible with Bionicle sets. But despite this, the story is continuing in serials written by Greg Farshtey online at BIONICLEstory.com .
The Bionicle franchise has been well received, with one reviewer describing the sets as "good combination of assembly and action figure" and first-year sales of 100 million British pounds (161.7 million USD). Bionicle had received a Toy of the Year Award for Most Innovative Toy in 2001 from the Toy Industry Association.
In 2001, several Māori tribal groups from New Zealand threatened legal action against Lego for allegedly trademarking Māori words used in naming the Bionicle product range. In response, a Lego spokesperson stated that only the term "Bionicle" had been trademarked. Lego agreed to stop commercial use of the Māori language after sending an executive to meet with Māori representatives in New Zealand. Some Māori terms used by Lego were changed, such as "Huki", which was changed to "Hewkii", and "Tohunga", which was changed to "Matoran". Within the fictional Bionicle universe, these changes were explained by the introduction of a "Naming Day" holiday, in which characters who have done heroic deeds for their village are honored by having the spelling of their name changed (though the pronunciation remains the same). However, a number of Māori terms such as "Toa", which means "warrior", "Kanohi", which means "face", and "Kopaka", which means "cold", were not changed. Since this controversy, Lego has not made any more names that are common terms in other living languages (with the exception of Umbra, a Latin word, and some names that are real names in some languages).
The rapid success of Bionicle has had a major impact on the Lego company. According to Stephanie Lawrence, the global director of licensing for Lego, "We've created an evergreen franchise to complement the many event-based properties on the children's market. An increasing number of category manufacturers want to tap into the power of the BIONICLE universe, and the key for us now is to manage the excitement to stay true to the brand and the lifestyle of our core consumer." According to one source, Bionicle has changed the way children think of, and play with, LEGO products by combining "the best of LEGO building with the story telling and adventure of an action figure line," and that 85% of American boys age 6–12 know of the Bionicle brand and 45% own the toys.