"Deca-Dence" is set in a post-apocalyptic world where humanity is on the brink of extinction due to the emergence of monstrous creatures known as Gadoll. The remnants of humanity survive within a massive mobile fortress called Deca-Dence, which serves as both a home and a defense mechanism against the Gadoll. The society within Deca-Dence is rigidly divided into two classes: the Gears, who are skilled fighters tasked with battling the Gadoll, and the Tankers, who handle maintenance and support roles. The Gears are celebrated as heroes, while the Tankers are often marginalized and viewed as expendable.

The protagonist, Natsume, is a young Tanker who dreams of becoming a Gear despite her physical limitations. Her father, a former Gear, was killed by the Gadoll, fueling her determination to fight. Natsume's life changes when she encounters Kaburagi, a gruff and experienced repairman who secretly works as a "cleaner" for the system that governs Deca-Dence. Kaburagi is tasked with eliminating anomalies that threaten the stability of the fortress, but he begins to question his role after forming a bond with Natsume.

As the story progresses, it is revealed that Deca-Dence is not merely a fortress but a constructed reality within a larger system. The world is a simulation controlled by a corporate entity called Solid Quake, which uses the fortress as a theme park for cyborgs who participate in battles against the Gadoll for entertainment. The Gadoll themselves are artificial creations designed to provide challenges for the cyborgs, while the human inhabitants of Deca-Dence are unaware of the true nature of their world.

Natsume and Kaburagi's relationship becomes central to the narrative as they uncover the truth about Deca-Dence and the exploitation of humanity. Kaburagi, who was once a loyal enforcer of the system, begins to resist its control, while Natsume's determination to fight for a better future inspires others to question their roles. Together, they challenge the oppressive system, leading to a climactic confrontation that forces both humans and cyborgs to reconsider their place in the world.

The series explores themes of free will, resistance against systemic oppression, and the blurred lines between reality and illusion. Natsume's idealism and Kaburagi's cynicism create a dynamic interplay that drives the story forward, as they navigate a world where the boundaries between truth and deception are constantly shifting. The narrative balances action, mystery, and emotional depth, culminating in a resolution that redefines the future of Deca-Dence and its inhabitants.