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.

Having reached his emotional breaking point, Rintarou Okabe refuses to continue aiding time traveler Suzuha Amane in her mission to prevent World War III, believing any further efforts to save Makise Kurisu will be in vain. Shortly after, Okabe abandons his mad scientist persona and becomes a seemingly regular university student. Okabe's close friend Mayuri Shiina perceives him to be recovering from his trauma and is visibly happy. However, something still seems to be bothering Okabe. Steins;Gate: Kyoukaimenjou no Missing Link - Divide By Zero marks the beginning of a critical divergence—a timeline in which the burden of fate escalates beyond one's limits.

Eccentric scientist Rintarou Okabe has a never-ending thirst for scientific exploration. Together with his ditzy but well-meaning friend Mayuri Shiina and his roommate Itaru Hashida, Okabe founds the Future Gadget Laboratory in the hopes of creating technological innovations that baffle the human psyche. Despite claims of grandeur, the only notable gadget the trio have created is a microwave that has the mystifying power to turn bananas into green goo. However, when Okabe attends a conference on time travel, he experiences a series of strange events that lead him to believe that there is more to the Phone Microwave gadget than meets the eye. Apparently able to send text messages into the past using the microwave, Okabe dabbles further with the time machine, attracting the ire and attention of the mysterious organization SERN. Due to the novel discovery, Okabe and his friends find themselves in an ever-present danger. As he works to mitigate the damage his invention has caused to the timeline, Okabe fights a battle to not only save his loved ones but also to preserve his degrading sanity.

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.