In ancient Disboard, Riku is an angry, young warrior intent on saving humanity from the warring Exceed, the sixteen sentient species, fighting to establish the "One True God" amongst the Old Deus. In a lawless land, humanity's lack of magic and weak bodies have made them easy targets, leaving them on the brink of extinction. One day, hope returns to humanity when Riku finds a powerful female Ex-machina, whom he names Schwi. Exiled from her Cluster because of her research into human emotions, Schwi is convinced that humanity has only survived due to the power of these feelings. Forming an unlikely partnership in the midst of the overwhelming chaos, Riku and Schwi must now find the answers to their individual shortcomings in each other, and discover for themselves what it truly means to be human as they fight for their lives against all odds. Each with a powerful new ally in tow, it is now up to them to prevent the extinction of the human race and establish peace throughout Disboard!
In the distant technological future, civilization has reached its ultimate Net-based form. An "infection" in the past caused the automated systems to spiral out of order, resulting in a multi-leveled city structure that replicates itself infinitely in all directions. Now humanity has lost access to the city's controls, and is hunted down and purged by the defense system known as the Safeguard. In a tiny corner of the city, a little enclave known as the Electro-Fishers is facing eventual extinction, trapped between the threat of the Safeguard and dwindling food supplies. A girl named Zuru goes on a journey to find food for her village, only to inadvertently cause doom when an observation tower senses her and summons a Safeguard pack to eliminate the threat. With her companions dead and all escape routes blocked, the only thing that can save her now is the sudden arrival of Killy the Wanderer, on his quest for the Net Terminal Genes, the key to restoring order to the world.