Guilty Crown's setting begins in 2029 when an unidentified "Apocalypse Virus" spreads and plunges Japan into a state of emergency in an chaos known as the "Lost Christmas". An international organization known as the GHQ intervenes with martial law and restores order to Japan at the cost of its independence.

Ten years later in 2039, Shū Ōma, a 17-year-old high school student who keeps to himself in school, meets Inori Yuzuriha, the lead singer for Egoist, while visiting one of his favourite places on his way home from school. Shū is a big fan of Inori, a singer who has taken the Internet world by storm. However, he also discovers the other side of her, which is that she is a member of "Undertaker", a resistance group that aims to liberate Japan from the GHQ. Shū starts taking a part in the actions of "Undertaker" and the "king's mark" appears on his right hand. This "mark" bestows on him the power to draw out a weapon from another person.