The 2001–2008 storyline arc of Bionicle was set in a science fantasy world inhabited predominantly by part-organic, part-machine beings with souls. The subterranean world is contained in massive underground domes, which reside in the massive robot body of Mata Nui. This world (dubbed "The Matoran Universe") and its races were once protected by a Great Spirit named Mata Nui, until he was cast into an eternal sleep by the evil Makuta Teridax and the Brotherhood of Makuta. The world of the Matoran eventually fell under the rule of Makuta Teridax. But a team of Toa called the Toa Nuva had reawakened Mata Nui. They soon realized that while Mata Nui was sleeping Teridax had taken control of his body. Now the Mask of Life that was stored inside Mata Nui, now containing his very spirit, was shot out of his body by Teridax, who had just gained control of the Matoran Universe.. The mask landed on the planet of Bara Magna, and the mask created a smaller body for Mata Nui.
2009 began a whole new saga of the story-line, leaving behind the previous years, and venturing out to newer possibilities as Mata Nui, after having been banished by Makuta Teridax, crash lands on a mysterious barren planet, called Bara Magna. Here he becomes the center of the story, and makes new allies as he tries to find a way to save the Matoran and the Toa from Makuta Teridax's tyrannical rule.
2001 – Quest for the Masks
The story begins with six Toa Mata—Tahu, Lewa, Gali, Kopaka, Pohatu, and Onua—who arrive on the Island of Mata Nui in silver canisters, remembering nothing beyond their names and scraps of disturbing dreams. They discovered that the inhabitants, the Matoran villagers, face relentless attacks from infected Rahi, savage beasts controlled by the powerful influence of Makuta Teridax through use of Infected Kanohi masks, causing a period of terror which lasted about 1000 years. This was brought to an end by the brave actions of the wandering outcast Takua, who gathered together the six Toa stones to finally summon the Toa Mata to the island. The Toa then joined the war for a month, searching for and finding numerous Kanohi masks, before they all received Golden Kanohi with tremendous power, and descended below ground to face Makuta himself. After challenging the ferocious Manas crabs and the Shadow Toa (evil doppelgänger-like illusional replicas of the Toa ), the Toa confront Makuta and, by uniting their elemental powers, defeat him and return to the surface. But Makuta was only testing their powers and would return.
2002 – The Bohrok Swarms
Upon his defeat, Makuta released the ancient Bohrok, robotic drones designed to "cleanse" the island of Mata Nui to its state "in the before-time". The Bohrok began to tear through the villages on the island, forcing Matoran to flee. One inventive Matoran of Earth, Nuparu, builds a powerful vehicle called the Boxor, made from parts of a damaged Bohrok in order to fight off the swarms. The Toa, unaware of the Bohrok's purpose, collected the Bohrok's Krana (mask-like creatures that function as their brains) to confront the Bohrok Queens, the Bahrag: Cahdok and Gahdok. The battle results in the queens' becoming sealed in a prison of "protodermis", created by fusing the elemental powers of all six Toa. The Toa Mata were then dropped into energized protodermis, which transformed them, granting them new armor, weapons, and a new name: the "Toa Nuva".
2003 – The Bohrok-Kal Strike / Mask of Light
After the defeat of the Bohrok Queens, the Toa Nuva and Matoran begin to use the Bohrok to rebuild their villages on Mata Nui. However, six new elite Bohrok, the Bohrok-Kal, appeared with the purpose of releasing the Bahrag. Their presence was first noticed when the Bohrok swarms oddly returned to sleep in their hives and the Toa were no longer able to control the elements. The Bohrok-Kal had stolen the six elemental symbols that granted the Toa Nuva the ability to control the six elements. The Kal must use these stones to unlock the Bahrag from their prison, but as they began to place these keys, the Toa Nuva of fire, Tahu, used the Mask of Time, a powerful hidden mask that slowed down time long enough for the Toa to come up with the plan of focusing all their energy into the stone tablets. The stone tablets then began to give off power to the Bohrok-Kal, making them unimaginably strong and arrogant, with dreams of leading the Bohrok swarms themselves rather than freeing the Bohrok Queens. However, their newfound power exceeded their control as the Toa Nuva continued to feed it to them through the tablets. Eventually, each of the six Bohrok Kal fell victim to a horrible demise created by their own out-of-control powers, allowing the Toa Nuva to regain their abilities of elemental control and bringing peace at last to the island of Mata Nui. However, this peace would not last.
Several weeks later, two Matoran, Takua and Jaller, discovered the Kanohi Mask of Light. Vakama, Turaga (elder) leader of their village of Ta-Koro, tasked the duo with traveling across the island of Mata Nui to find the Mask's owner: the seventh "Toa of Light", prophesised to defeat Makuta, and begin the process that would awaken Mata Nui. Makuta responded by creating six creatures called "Rahkshi" from his essence, tasking with finding and killing the herald of the Toa of Light. The Rahkshi tore across Mata Nui, destroying the villages of Ta-Koro and Onu-Koro. The Rahkshi were defeated in battle at the great temple Kini Nui by the Toa, but not before killing Jaller. Jaller's death caused Takua to realize that he was the Toa of Light, not the Herald, and he donned the mask to become Toa Takanuva. Takanuva went to confront Makuta and, during their battle, they both fell into a pool of energized protodermis and became fused together into the being Takutanuva. Takutanuva then proceeded to open the door to the city of Metru Nui, allowing the Matoran and Toa through. Using some of his life energy, he revived Jaller while still holding the door open. However, the use of energy was too great and Takutanuva was crushed by the door, appearing to kill both Takanuva and Makuta, leaving only Takanuva's Mask of Light. Vakama, Jaller, and fellow Matoran Halhi manage to revive Takanuva, using his mask to activate the beacon to Metru Nui, an island city that Makuta had prevented the Matoran from reaching. With Makuta gone, the Matoran prepared to return to that city, just as the Turaga revealed a shocking truth to the Toa Nuva: they were not the first Toa.
2004 – Legends of Metru Nui
As the Matoran prepared to journey to Metru Nui, the Turaga (village elders) revealed that they had once been Toa, fighting in Metru Nui against threats to the Matoran in the last days of the city's golden age. Metru Nui had known peace under the leadership of Turaga Dume and the city's guardian Toa Lhikan, but this changed when Lhikan was kidnapped by two mercenaries, who were part of a group called the Dark Hunters. Before his kidnapping, Lhikan chose 6 Matoran to take his place, and made Toa stones using some of his power to turn them into Toa. The 6 Matoran thus became the Toa Metru, and set out to find the six Great Disks that were the key to defeating the Morbuzakh, a plant menace that threatened to destroy the city. When they did, however, they were betrayed by Dume, who had secretly arranged the kidnapping of Lhikan himself. Three Toa were captured, and the others were pursued across Metru Nui by the dark Hunters and the city's robotic law enforcers the Vahki. After rescuing their captive brothers, and finding Lhikan, now a Turaga, the Toa discovered that Makuta Teridax, who had been assigned to protect the city, had captured Dume and taken his place. This was part of his plan to put the Matoran to sleep, wipe out their memories, and reawaken them "as their conqueror." On the night the Toa confronted Makuta, the last Matoran were captured, and Mata Nui was finally put to sleep, beginning the event known as the Great Cataclysm that devastated Metru Nui. The Toa fled with as many Matoran as they could carry, but were attacked by Makuta. Combining their elemental powers, they were able to seal Teridax in a prison of crystallized protodermis, though not without the sacrifice of Lhikan. The Toa traveled to an island far above—the island of Mata Nui, as it would later be named—vowing to return to save the remaining Matoran. On their journey, they found many dangers, such as the long lost Matoran Mavrah, prehistoric Rahi, and the early prototypes for the Vahki—the Krahli. The Toa Metru chose sites for their villages and hid the Great Masks of Power the Toa Mata and Toa Nuva would find in their time, as well as the six Toa stones that would eventually summon the Toa Mata. With their preparations complete, the Toa Metru began their return journey to Metru Nui, to save the Matoran still trapped.
2005 – Web of Shadows
Upon the Toa Metru's return to Metru Nui to rescue the remaining Matoran, they found the city in ruins. In their absence, the evil king Sidorak and his viceroy Roodaka, agents of the Makuta, had been reigning in terror on the devastated island, with vicious spider-like creatures called Visorak overrunning the city and mutating everything that lives. The Toa were soon captured and mutated into bestial half-Toa half-Rahi Toa Hordika. The Rahaga, mysterious beings who capture Rahi in a bid to protect them from the Visorak, rescue the newly mutated Toa from falling from their cocoons to their deaths. They explain that to revert to normal, the Toa Hordika must seek out Keetongu, a legendary Rahi rumored to be knowledgeable in venoms and their counter-agents. Deciding to put their conditions to one side, the Toa work with the Rahaga to build airships to evacuate the Matoran. The Rahaga reveal that they were once the Toa bodyguards of Makuta Teridax, but they betrayed their master after learning of his plans to enslave the Matoran, and stole the Mask of Light, though at the cost of being mutated by Roodaka into their present twisted forms. After the Toa Hordika retrieved the Mask of Light from where the Rahaga hid it, Toa Vakama, guilt-ridden by his failure to protect his teammates, succumbed to his Rahi impulses and betrayed the other Toa to join Sidorak, who made him the leader of the Visorak. The other Toa, after enlisting Keetongu's support, confronted the Visorak horde in a great battle, during which fellow Toa Matau convinced Vakama to rejoin them. Vakama then ordered the Visorak to be free. Meanwhile, Keetongu killed Sidorak, whom Roodaka and Vakama betrayed. The six Toa then defeated Roodaka with all six of their elemental powers. Unknown to the Toa, Roodaka carried a shard of Makuta's prison within her armor. When the shard was destroyed by the Toa's elemental assault, Makuta's prison was destroyed as well, freeing the master of shadows. Having been restored by Keetongu, the Toa Metru, Rahaga, and Keetongu load up airships with the Matoran pods to bring to the island above. The leader of the Rahaga, Norik, thanks Vakama for letting him see a legend come true: the Great Rescue of the Matoran. On their way to Mata Nui, Vakama jumps out of the airship to retrieve the Mask of Time. After locating and repairing minor damage on the mask, Vakama is attacked by Voporak, a temporal-sensitive employed by the Dark Hunter organization. Vakama is knocked unconscious, and falls into the sea. Makuta finds him and rescues him, believing Vakama to have hidden the mask. To discover its location, Makuta casts Vakama into an illusion. After waking up, he eventually realizes flaws within the illusion and manages to free himself. He and Makuta, commanding a small troop of Rahkshi, form a truce to retake the Mask of Time from The Shadowed One, whom Voporak serves, and his bodyguard Sentrakh. During the ensuing conflict, which Keetongu joins in an attempt to kill Makuta, Voporak and Sentrakh are incapacitated and the Shadowed One crippled. Vakama steals the mask and attempts to flee, but the Shadowed One damages Vakama's jetpack with his eyebeams. Makuta pursues Vakama to the Great Furnace of the city's fire district. In lieu of Vakama's threat of destroying the mask, Makuta agrees to Vakama's terms of a year of peace with the Matoran and teleports Vakama to the island of Mata Nui, content to know the location of the mask. After hiding the Mask of Light, The Toa then proceed to awaken the Matoran by sacrificing their Toa and elemental power. Now Turaga, they christen the island Mata Nui and direct the Matoran to build the villages, knowing that Makuta would return to wage war, which would only end with the prophesised arrival of the Toa Mata.
2006 – Island of Doom
After returning to Metru Nui, the Toa Nuva learned that the great Spirit Mata Nui was not only asleep but dying. To save him, they must travel to the island of Voya Nui and seek the mysterious Kanohi Ignika, the Mask of Life. The Toa Nuva set out on this adventure but were quickly taken prisoner by six new and powerful enemies, former Dark Hunters now calling themselves the Piraka: Zaktan, Hakann, Vezok, Thok, Reidak, and Avak. They sought the mask for their own dark purposes. When the Toa failed to return, a group of six Matoran followed after them. Jaller, Hahli, Hewkii, Nuparu, Kongu, and Matoro escaped to the island in Toa canisters; as they traveled, bolts of lighting from the Red Star transformed them into the Toa Inika. Upon their arrival, they learn of the Piraka and how they enslaved the local Matoran by posing as false Toa, in order to make the Matoran build them a fortress. With the help of a small Matoran Resistance and the ancient guardian Axonn, the Toa Inika were able to free the Toa Nuva, find the temple of the mask, and battle the Piraka as well as the other creatures guarding it (including Vezon, on which the Ignika was fused to). They eventually emerged victorious with the Kanohi. But the Mask of Life possessed a will of its own, and in the last moment evades them all, dropping into the depths of the sea.
2007 – Sea of Darkness
Chasing after the Mask of Life, the Toa Inika descended into the waters after receiving the mysterious clue "save the sunken city" from an unknown Matoran, who had saved Hahli from drowning at the cost of her dying from decompression sickness. A burst of energy from the Mask of Life transformed the Toa Inika into water-breathing Toa Mahri. They discovered the inhabited village of Mahri Nui that had broken off from Voya Nui and sunk a thousand years ago. The village was threatened by ancient warlords known as Barraki that had been mutated by the nearby mutagenic waters of "the Pit". The Toa Mahri faced off against the Barraki to survive, as well as discovering that the Makuta had survived his supposed death, and had followed the Toa beneath the waves, possessing a robotic prison guard called Maxilos. However, by the time the Toa retrieved the mask, the Great Spirit died. Realizing there was still hope, Toa Matoro rushed to the core of the universe and revived Mata Nui by wearing the Mask of Life—a suicidal act. In his last moment, Toa Matoro used the Mask's power to teleport the Toa Mahri back to Metru Nui and allow them to breathe air again. Makuta, meanwhile, having fought against the vast marine armies of the Barraki, was once again presumed dead. The Great Spirit's life was saved, but he remained asleep—it fell now to the Toa Nuva to wake Mata Nui.
2008 – The Final Battle
After being equipped with new armor and weapons by Artakha, the Toa Nuva arrived at Karda Nui, the core of the world glimpsed previously by the late Toa Matoro. There, they find the "Brotherhood of Makuta" 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 darkness because of a shadow leech attack; and Toa Ignika, a Toa-like manifestation of 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, and because it was inspired by Matoro to become a hero. With their combined forces, they reached a structure in the center of Karda Nui called the "Codrex", the place where the Toa Mata were originally held in hibernation, to be released in the event of Mata Nui falling asleep. Takanuva, with the help of the remaining uncorrupted Av-Matoran, returned the Shadow Matoran to their previous states. Shortly afterwards, Ignika sacrificed his new body to awaken Mata Nui on behalf of the Toa Nuva, as the original process would have been too slow and would have trapped the Toa Nuva inside the Codrex. The 7 Toa then 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 Makuta had taken over Mata Nui's body. Trapping the spirit of Mata Nui in the Ignika, Makuta shot the mask into space, so that the former Great Spirit cannot interfere with his control over the universe. In the epilogue, the Ignika is seen flying through space, with Mata Nui inside, thinking only one thing: "I will return."
2009 – The Legend Reborn
Following Mata Nui's banishment from his body by Makuta Teridax, the arc starts with the Ignika crashing onto Bara Magna, a vast, mostly-barren planet. With the exception of a few wildlife species, Bara Magna is a desert planet which only supports few resources, so each tribes 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. Four of the tribes have co-existed peacefully, though the Sand Tribe has not, and its members have regressed into beasts. Recently, however, the arrival of the Rock tribe has upset the balance, as their warriors, known as Skrall, win every fight they participate in. Just as the Skrall prepare to wage all-out war with the other tribes, the Ignika lands on Bara Magna, creating 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 bandits called the Bone Hunters and look for a way to return to his body. With the help of his new Glatorian and Agori friends, he exposes a traitor who attempts to seize power after Mata Nui defeats the Skrall's leader in single combat. Mata Nui, after turning the traitor into a snake, fights with his allies to defeat the Skrall and Bone Hunters with help from the Scarabax (robotic bug like creature), along with an army of Glatorian led by veterans Ackar, Tarix and Vastus. Mata Nui helps the villages of the world unite, taking all of the giant mechanical pieces that make the villages and linking them into a large prototype robotic body, a body like the one the Matoran Universe resides in.
2010 – Journey's End
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. Tarduk, an Agori of Tesara, helps Mata Nui by showing him an ancient, yet unstable power source that can 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, as Mata Nui uses the body of the Agori robot to fight Teridax in Mata Nui's body. The golden armour, scattered by Makuta's blast is collected by Tahu, Gresh, and Takanuva from the many enemies. Tahu defeats Nektann, 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. When Teridax wants to continue the fight, he was momentarily weakened by the destruction of his Rahkshi legions. Mata Nui took advantage of the distraction, pushing Teridax back into one of the onrushing fragments of the moon Aqua Magna, whose impact destroys his core processor, killing Teridax. Mata Nui then mourns the brother that he could have had, in his mind.
The finale concludes when Mata Nui uses the last of his strength, and the power of the Ignika, 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 of the power core destroys 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, telling them that the future is their own 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 after the 2010 sets were finalized for release. Originally, Lego Ben 10 was possibly Bionicle's replacement, it got a replacement in 2010 called Hero Factory, a Lego theme compatible with Bionicle sets. But despite this, the story was continuing in serials written by Greg Farshtey online at BIONICLEstory.com, until Greg temporarily stopped writing due to being occupied with family obligations. BIONICLE.com and BIONICLEstory.com were shut down on June 19, 2013.