Only 3000 humans remain after three apocalyptic events, referred to as the "Catalysts", severely decreased the population. Catalyst One resulted in the air being toxic to breathe, so everyone wears masks. After the collapse of the government, various organizations have formed, and fight each other for territory and resources.

Oliver Naut is a scrappy kid who has grown up alone in the Deadzones — the most toxic areas on the planet — with nothing but the robotic swords in his arms for protection. But now he's teamed up with Namo, a skilled ex-assassin, to prevent an army of robotic soldiers from falling into the hands of the organizations, who will only use them for more violence and death. Will Oliver be able to bring humanity together to fight for peace instead?

Catalyst Wake is a linear visual novel. Instead of the typical "sprites against backgrounds" format, the dialogue is accompanied by illustrations, which gives it a cinematic quality. It's much like a motion comic.

It's a continuation of a series of animations and comics that were released between 2011 and 2016 that will finally conclude the story.