Six months after leading the resistance to victory and dismantling the Architect regime, Alice Chen, now Director of Daybridge's provisional government, finds her city in peril once more. A mysterious spontaneous enhancement outbreak is sweeping through the population, escalating from minor perceptual anomalies to widespread chaos and the collapse of Daybridge's financial center. Alice and her closest ally, the newly enhanced Ethan Reeves, trace the contagion to a sealed Architect vault within Helix Tower, which contained experimental, self-propagating enhancement prototypes that were deemed too dangerous even by the Architects themselves. As the enhancement rapidly evolves, becoming airborne and actively "hunting" new hosts, Alice faces the terrifying realization that her fight for freedom may have inadvertently unleashed a dormant legacy far more perilous than any tyranny: "The Awakening".

The desperate search for answers leads Alice and Ethan to discover shocking truths about humanity's past: humanity was not naturally evolved but designed and "translated" from a dying reality by an ancient being known only as The Original. The legendary Great Sundering, a cataclysm that destroyed previous civilizations, was a deliberate "reset" by The Original's failsafe, triggered to prevent a catastrophic dimensional breach caused by an external entity from "between realities". Now, a mysterious new faction, The Disciples of the New Dawn, led by the enigmatic Aurora and guided by this same entity (The Ancient One/Harbinger), plans a pilgrimage to The Cradle—humanity's secret birthplace and template storage—to initiate a final "ascension" that threatens to repeat the Sundering on a global scale. With Ethan uniquely connected to the rapidly evolving "lattice" of enhanced consciousness and Alice representing conventional humanity, they must find a middle path to guide humanity's evolution responsibly, or face the stark choice between transcendence or annihilation as the Architects' complex and cosmic legacy unfolds