Makuta Teridax is dead.
Several years have passed since his fall, and months after the conclusion of the Second Core War, which took away the six Toa Nuva. The Order of Mata Nui, led by the first Toa, Helryx, has emerged from the shadows and become official, tasked with overseeing the cohabitation of Matoran and Agori. However, in recent times, a series of thefts of Protodermis, and more importantly, of individuals, has begun to destabilize the delicate balance between the two peoples.
The Unity War, between Matoran and Agori, is occurring in secret, without the involvement of their traditional protectors: the Toa (including Inika and Hagah) and the Glatorian. Helryx initiates a secret meeting on New Daxia with two key allies, Ackar and Kiina, who were also close friends of Mata Nui before the final battle against Makuta Teridax on the soil of Bara Magna. Her goal is to reinforce the alliance with Certavus' Army under Ackar's command, who is no longer the leader of the Agori.
Raanu, the new ruler of the United Villages, seeks to eliminate every Matoran threat from any village, claiming that these lands belong solely to the Agori. Meanwhile, in Roxtus, the Turaga of Metru Nui (Vakama, Nokama, Matau, Nuju, Onewa, and Whenua) awaken inside an ancient temple, transformed into Toa once more. This transformation is biologically impossible. A mysterious, inverted clover-like symbol on each of their shoulders appears to be a clue, perhaps leading to the individual or group responsible for the phenomenon.
Meanwhile, in Makuhero City, home of the famous Hero Factory militia, the founder of the Heroes, Akiyama Makuro, invites Alpha leader Preston Stormer to speak with members of the Order of Mata Nui, showing him the symbol of the Ignika, the Mask of Life, now in Helryx's possession. Months after the end of the Second Core War, a global conflict that allowed the Order and others to discover key truths about the infamous Great Beings, the Heroes landed on Spherus Magna, promising only peaceful research missions.
The planet that hosts Makuhero City and the Solis Magna system, home to Spherus Magna, is light-years apart. A significant time discrepancy also exists: time flows much more slowly within Solis Magna. To facilitate communication, special satellites engineered by Makuro bridge the gap. He appears to know much about biomechanical history and is particularly interested in the relationship between Protodermis and Quaza, the energy source of the Heroes. Not coincidentally, the latter was promised to locals—Matoran and Agori alike—to aid in rebuilding after the war.
The sites where Heroes have settled are called Checkpoints. At one such location, near Tesara, the young Hero Nex, dispatched with Stormer and Stringer, is killed by a mysterious green-armored creature. William Furno, Alpha Team member, upon hearing the news, mobilizes a large Hero force alongside Breeze and Surge to journey to planet 1210, also known by the Heroes as Spherus Magna.
Simultaneously, Fortis, commander of the elite Recon Team (which includes Rocka, Furno's rival for the Alpha Team leadership), begins a secret mission in Roxtus—both he and Furno equipped with Ultimate Armor, the final combat model designed by Makuro for biomechanical threats.
As Nokama, traveling with Matau, is kidnapped by unknown individuals, and a fearful Vakama tells Nuju about visions of a new, faceless threat, Whenua and Onewa arrive at the ruins of a city they believe to be Toka-Nui. There, they discover countless corpses of Matoran and Rahi scattered through the streets. The culprit? The Hero Factory. A massive "H," fragmented across buildings, claims responsibility, suggesting Makuro's direct involvement.
Not long after, the two Toa encounter a distant figure: it's Mazeka, the Order's spy. He leads them to a cave where they meet Tobduk, another agent of Helryx. Their questions about how a Turaga could revert into a Toa are met with answers that plunge Whenua and Onewa into deeper dread.
Meanwhile, Nokama awakens inside a strange airship, its interior reminiscent of Le-Metru. She's been kidnapped by the Heroes, led by Daniel Rocka. After initial friction, Nokama learns of the war between biomechanical beings and Heroes. She and Rocka strike a deal: he will recount how the conflict began.
Rocka explains how he and Fortis' team hunted the enemy in the Black Spike Mountains in Roxtus, while Tobduk and two Order's Matoran, Orkahm and Ehrye, fought alongside Ruhnga soldiers against terrifying eastern beasts. The villages of Iconox and Tesara suffered the worst.
Simultaneously, the Heroes' HQ at Skrall River, where a major summit involving Stormer, Furno, Breeze, and Surge was underway, is attacked by the same creatures, led by the one that killed Nex. This monster demands the return of the Spear of Rewerax, now in Hero's hands. Thanks to their Hero Jets still orbiting the planet, the HQ narrowly repels the attack. However, the Order and Certavus' Army endure a much longer battle near Wha-Nui.
Eventually, Mazeka reveals he witnessed mysterious figures in the Shadowed One's former throne room during a secret mission. In the end, the truth comes out: under orders from Helryx and Turaga Dume, the populations have returned inside the giant Robot, once controlled by Makuta Teridax during his final confrontation with his "brother" Mata Nui. Everything that happened on Spherus Magna, including the eastern monsters' attacks, took place in the past, while the rebirth of the Turaga as Toa Metru is occurring in a present undefined within the restructured Matoran Universe.
But how could this have happened?
Before reaching the Toa Metru, there's one final piece of the puzzle. One last story that Tobduk and Mazeka must tell about five protectors, personally chosen by Toa Helryx shortly after the return into the Robot…