"Synduality" is set in a dystopian future where humanity faces existential threats from mysterious, hostile entities known as "Enders." These creatures have driven humans to the brink of extinction, forcing survivors to take refuge in underground cities. The surface world has become a dangerous wasteland, and humanity's survival hinges on advanced technology and the use of specialized combat units called "MAGUS," which are piloted by individuals known as "Drifters."

The narrative centers on Kanata, a young Drifter who operates in the hazardous surface world to scavenge resources and protect humanity's remnants. Kanata pilots a MAGUS unit named Noir, an advanced AI with a unique personality and combat capabilities. Noir's sentience and evolving relationship with Kanata form a core element of the story, exploring themes of trust, partnership, and the boundaries between human and machine.

As Kanata and Noir undertake missions to secure vital supplies and fend off Enders, they encounter other Drifters and factions with conflicting agendas. Among these is a mysterious girl named Alice, who possesses knowledge about the origins of the Enders and the true nature of the MAGUS units. Her presence introduces a layer of intrigue, as her motives and connection to the broader conflict remain ambiguous.

The series delves into the political and social dynamics of the underground cities, where power struggles and resource scarcity create tension among survivors. Factions vie for control over MAGUS technology, and ethical dilemmas arise regarding the use of AI in warfare and the potential consequences of humanity's reliance on machines.

Throughout the story, Kanata and his allies face escalating threats from both the Enders and human adversaries, uncovering secrets about the world's collapse and the role of MAGUS units in shaping the future. The narrative balances action-driven sequences with moments of introspection, examining the resilience of humanity and the evolving relationship between humans and AI in a world on the brink of annihilation.