High above the realm of man, the gods of the world have convened to decide on a single matter: the continued existence of mankind. Under the head of Zeus, the deities of Ancient Greece, Norse mythology, and Hinduism, among others, call assembly every one thousand years to decide the fate of humanity. Because of their unrelenting abuse toward each other and the planet, this time the gods vote unanimously in favor of ending the human race. But before the mandate passes, Brunhild, one of the 13 demigod Valkyries, puts forth an alternate proposal: rather than anticlimactically annihilating mankind, why not give them a fighting chance and enact Ragnarök, a one-on-one showdown between man and god? Spurred on by the audacity of the challenge, the divine council quickly accepts, fully confident that this contest will display the utter might of the gods. To stand a chance against the mighty heavens, Brunhild will need to assemble history's greatest individuals, otherwise the death knell will surely be sounded for mankind.

After the death of his parents, a young Mirai Kakehashi is left in the care of his abusive relatives. Since then, he has become gloomy and depressed, leading him to attempt suicide on the evening of his middle school graduation. Mirai, however, is saved by a pure white girl named Nasse who introduces herself as a guardian angel wishing to give him happiness—by granting him supernatural powers and a chance to become the new God. In order to earn the position, he must defeat 12 other "God Candidates" within 999 days. Soon, Mirai begins a struggle to survive as a terrifying battle royale erupts between himself and the candidates looking to obtain the most power in the world.

Tamahiko Shima is the youngest son of the powerful and wealthy Shima family. Blessed with great fortune since his childhood, he grew up wanting nothing but affection from his oftentimes distant family. After losing his mother and crippling his dominant arm in an accident, Tamahiko fell into deep despair and is cast aside by his own father for his handicap. Condemned to live isolated in the countryside where he would not bring shame to his family's name, he resigned himself to dying alone—until one day, a young girl named Yuzuki Tachibana appeared on his doorstep, proclaiming that Tamahiko's father sent her to be his bride. As she takes care of Tamahiko, Yuzuki brings a feeling of springtime into Tamahiko's dreary life, allowing him to gradually heal from the deep emotional scars of his youth. Their lives slowly intertwine as both Tamahiko and Yuzuki taste the fruits of their first love.