Since the death of his parents, Shinpei Ajiro had lived with the Kofune family and their two daughters—Mio and Ushio. Although he then left his home island to continue his education in Tokyo, Shinpei returns after Ushio tragically drowns during the attempted rescue of a little girl. During the funeral, his best friend informs him about bruises found around Ushio's neck, casting doubt over the cause of her death. Suspecting a murder has taken place, Shinpei reevaluates recent events, but strange incidents only continue to transpire. Disappearing people and other unexplainable occurrences lead Mio to recall an old folktale referring to entities called Shadows, which may not be entirely fantasy. Supposedly, an encounter with one's Shadow foretells the person's impending demise. Facing the dark side of Hitogashima Island, Shinpei stands against his grim fate to fulfill Ushio's final will—to protect Mio.

At Hope's Peak Academy, a school full of extraordinarily talented individuals, Nagito Komaeda is an ordinary boy with no special traits or interesting skills to speak of—except for his incredible unluckiness. Just walking to school in the morning leads to a number of unfortunate accidents, which only escalate as the day goes on. Despite this, Komaeda leads a relatively normal life and is satisfied with his modest slice of happiness. But everything changes when a mysterious boy who declares himself the Destroyer of the World arrives to shatter this hopeless paradise.

It is said that fireworks can calm the souls of the dead. For Tomoya Sugisaki, Aoi Harukawa, and Ryou Kobayashi, fireworks are what allowed them to meet the Summer Ghost. Believed to be the spirit of a young woman who committed suicide, the Summer Ghost only appears in a specific area and can only be seen by those who are within arm's reach of death. Tomoya is a creative soul being crushed by his academic obligation to get into a good university. Aoi is a meek girl who is relentlessly bullied by her classmates. Ryou is a former basketball star who had to forfeit his passion following a grim diagnosis. The only thing these three have in common is their ability to see the Summer Ghost. The Summer Ghost is said to be able to answer any and all questions pertaining to death—something the three teenagers desperately want to know more about. Dissatisfied with their initial meeting, Tomoya sets out to find the Summer Ghost once again. But the more time he spends with the ghost, the more the mystery surrounding her existence unravels.

OZ, a virtual world connected to the internet, has become extremely popular worldwide as a spot for people to engage in a large variety of activities, such as playing sports or shopping, through avatars created and customized by the user. OZ also possesses a near impenetrable security due to its strong encryption, ensuring that any personal data transmitted through the networks will be kept safe in order to protect those who use it. Because of its convenient applications, the majority of society has become highly dependent on the simulated reality, even going as far as entrusting the system with bringing back the unmanned asteroid explorer, Arawashi. Kenji Koiso is a 17-year-old math genius and part-time OZ moderator who is invited by his crush Natsuki Shinohara on a summer trip. But unbeknownst to him, this adventure requires him to act as her fiancé. Shortly after arriving at Natsuki's family's estate, which is preparing for her great-grandmother's 90th birthday, he receives a strange, coded message on his cell phone from an unknown sender who challenges him to solve it. Kenji is able to crack the code, but little does he know that his math expertise has just put Earth in great danger.