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. [Written by MAL Rewrite]

Mafia is rife in America where assassinations are a regular occurrence on the streets. Inferno, a mysterious company, is behind most of these dealings through the use of their near-invincible human weapon, "Phantom." One day, a Japanese tourist accidentally witnesses Phantom's latest murder. Desperate to escape, the tourist hides in a secluded building. However, Phantom, revealed to be a young woman named Ein, and the leader of Inferno "Scythe Master" captures the tourist and brainwashes him. Given the name "Zwei," this once peaceful tourist is now a puppet of Inferno with no memories. Drawn into a world of lies, deceit, and violence, Zwei must fight to survive, hopefully to one day regain his memories and escape from this world where he is constantly on the brink of death. [Written by MAL Rewrite]

Life back on the cruise following the Island Special Examination is anything but smooth sailing. Almost immediately after their return, the first-year students of Tokyo Metropolitan Advanced Nurturing High School face yet another special exam, with both class and individual points on the line. In addition to the complicated ruleset, more issues arise in the form of Kakeru Ryuuen and Kei Karuizawa. Angered by the previous test's outcome, Ryuuen is dead set on outdoing every class in the new challenge using any means necessary. Meanwhile, Karuizawa, a crucial pillar of Class D, is close to crumbling under the pressure of her past. The stage is now set for Kiyotaka Ayanokouji to once again—using the full extent of his planning, foresight, and ruthless manipulation—steer Class D to victory as dangerously close enemy forces try to bring it down. [Written by MAL Rewrite]