The eccentric, self-proclaimed mad scientist Rintarou Okabe has become a shell of his former self. Depressed and traumatized after failing to rescue his friend Makise Kurisu, he has decided to forsake his mad scientist alter ego and live as an ordinary college student. Surrounded by friends who know little of his time travel experiences, Okabe spends his days trying to forget the horrors of his adventures alone. While working as a receptionist at a college technology forum, Okabe meets the short, spunky Maho Hiyajo, who later turns out to be the interpreter at the forum's presentation, conducted by Professor Alexis Leskinen. In front of a stunned crowd, Alexis and Maho unveil Amadeus—a revolutionary AI capable of storing a person's memories and creating a perfect simulation of that person complete with their personality and quirks. Meeting with Maho and Alexis after the presentation, Okabe learns that the two were Kurisu's colleagues in university, and that they have simulated her in Amadeus. Hired by Alexis to research the simulation's behavior, Okabe is given the chance to interact with the shadow of a long-lost dear friend. Dangerously tangled in the past, Okabe must face the harsh reality and carefully maneuver around the disastrous consequences that come with disturbing the natural flow of time.

Devils cannot take form without a living host. However, if the will of an individual is strong enough, they can overcome the demon and make its power their own, becoming a Devilman. Weak and unassuming, Akira Fudou has always had a bleeding heart. So when his childhood friend Ryou Asuka asks for his help in uncovering devils, Akira accepts without hesitation. However, to Akira's surprise, the place they go to is Sabbath: an immoral party of debauchery and degeneracy. Amidst bloodshed and death, demons possess the partiers, turning their bodies into grotesque monsters, and begin wreaking havoc. In a reckless attempt to save his best friend, Akira unwittingly merges with the devil Amon and becomes a Devilman, gaining the power to defeat the remaining demons.Though it grants him great power, this new partnership awakens an insatiable and primeval part of Akira. Having the body of a devil but the same crybaby heart, Akira works alongside Ryou, destroying those that harm humanity and his loved ones.

In the mysterious future, crystalline organisms called Gems inhabit a world that has been destroyed by six meteors. Each Gem is assigned a role in order to fight against the Lunarians, a species who attacks them in order to shatter their bodies and use them as decorations. Phosphophyllite, also known as Phos, is a young and fragile Gem who dreams of helping their friends in the war effort. Instead, they are told to compile an encyclopedia because of their delicate condition. After begrudgingly embarking on this task, Phos meets Cinnabar, an intelligent gem who has been relegated to patrolling the isolated island at night because of the corrosive poison their body creates. After seeing how unhappy Cinnabar is, Phos decides to find a role that both of the rejected Gems can enjoy. Houseki no Kuni follows Phos' efforts to be useful and protect their fellow Gems.

Riko, daughter of the missing White Whistle Lyza the Annihilator, aspires to become like her mother and explore the furthest reaches of the Abyss. However, just a novice Red Whistle herself, she is only permitted to roam its most upper layer. Even so, Riko has a chance encounter with a mysterious robot with the appearance of an ordinary young boy. She comes to name him Reg, and he has no recollection of the events preceding his discovery. Certain that the technology to create Reg must come from deep within the Abyss, the two decide to venture forth into the chasm to recover his memories and see the bottom of the great pit with their own eyes. However, they know not of the harsh reality that is the true existence of the Abyss.

Having failed 19 job interviews in one day, Juri Yukawa's dreams of moving out of her parents' home are utterly dashed. Stuck living with her working mother Nobuko, NEET brother Tsubasa, laid-off father Takafumi, and single-parent sister Sanae, the only hope for this family to raise a decent adult is her little nephew Makoto. However, this struggling family's life takes a turn for the worse when Makoto and Tsubasa are violently kidnapped by a mysterious organization and held for ransom. With only 30 minutes to deliver five million yen to the criminals, Juri's grandfather reveals a dangerously powerful secret to her and Takafumi. By offering blood to her grandfather's mystical stone, the three enter the world of "Stasis," a version of their world where time stops for everyone but the users. Having arrived at their destination, their rescue efforts go awry when they are assailed by a surprising group of people who are somehow able to move around within Stasis. While all hope seems lost, a monstrous giant known only as the Herald appears amidst the chaos, its intent and motivations as cryptic as the very nature of this timeless world.