2041, Earth. After being pulled into the planet's atmosphere, the fall of the Freeport Space Station has led to the Great Cataclysm—an event that devastated the Earth's environment. Left as a polluted wasteland, survivors go to war with their fellows to guarantee themselves resources; in the end, these scrimmages have erased the whole existence of humanity. Coincidentally, life still exists on a moon base. Although it is supposedly meant as an immigration outpost for the mission to explore Mars, it is soon turned into a city, both regulating and allowing its citizens to flourish. The lunar base, officially named The City of Eden, holds the hope of fully colonizing the moon. Takeru, one of many citizens of Eden in the year 2267, participates in Tube Races between gangs and groups using hovercraft-like vehicles. Due to causing an accident in one of his races, Takeru is sentenced to complete volunteer work outside the city. While clearing his punishment, Takeru stumbles upon remains that may unravel the truth about Earth and Eden's genesis.

In the year 54 AD, 15-year-old slave fighter Cestvs desires one thing—an escape from his violent life. It is the wish Cestvs' owner has promised to grant him, but only after he wins 100 battles. However, Cestvs quickly comes to terms with the fact that, as a slave, his life is expendable. After the death of his friend, the possibility of freedom is the only thing keeping him going. With a burning ambition to attain it, Cestvs embarks on a journey to earn himself back, even if it means fighting other slaves for the entertainment of the public.

In 2024, the computer network prevails throughout daily life. Sora Yuuki is a 14-year-old girl. One day, she is invited to an online game The World. After an accident in the game, the real world begins to deform.

Shin Hazama has shut his heart ever since the mysterious and sudden death of his mother during his childhood. With his scientist father occupied with research, he can only rely on his childhood friend, Kotori Izumi, the popular and good-natured daughter of his father's employer. At the end of their third year of high school with graduation right around the corner, Shin and Kotori finally begin to move forward together, both in life and in love. Everything falls apart again when Shin's father also suddenly dies. But before things can settle down, he and Kotori learn the secret behind his parents' sudden deaths when they encounter agents from a high-tech dystopian Japan existing in a parallel universe. Among them is Jin, Shin's relative self, who is working against the humanoid weapons Miko and Niko. As the lives of relative selves are linked, Jin has two objectives: defend the vulnerable Shin to protect both their lives, and assassinate Kotori to end the ironclad rule of her relative self, Princess Kotoko—his mortal enemy and the killer of his parents. Confronted with this new reality, Shin and Kotori must honestly face their feelings for each other, even if the world as they know it will end tomorrow.