Set in the year 2039, Japan is the under the rule of a multinational military force called GHQ after the country went into chaos due to the "Lost Christmas" incident ten years prior to the start of the series, when a giant outbreak of an alien virus called the Apocalypse Virus spreads during Christmas, causing the United Nations to send the GHQ to contain the outbreak and restore order. The series follows Shu Ouma, an intelligent yet socially awkward teenager who finds himself caught in the war between the GHQ and "Funeral Parlor (Undertakers)", a resistance organization led by Gai Tsutsugami, which aims to liberate Japan from the GHQ, when he meets Inori Yuzuriha, the famous Internet Singer of the band Egoist and a member of the Undertakers. Due to various circumstances, Shu acquires a genetic weapon called the Void Genome, also known as "power of kings", which allows him to extract "Voids", objects with special properties that reflect the personality of their owners from underage individuals. With his new powers, Shu joins the Undertakers to protect Inori and learns secrets and mysteries he never knew.
Himari Takakura passes away after going out on a trip with her brothers, twins Kanba and Shōma. She was, however, miraculously saved by a spirit in a penguin-shaped hat. In return for her extended life, the twins must search for an item known as the Penguin Drum with the aid of three penguins, which are visible only to the siblings.
Haruka Kasugano and his twin sister Sora have lost both their parents in an accident, and with them all their support. They decide to move out of the city to the rural town where they once spent summers with their late grandfather. At first everything seems familiar and peaceful, but changes come as Haruka starts to remember things from his youth.