The Mizuhanome System is a highly advanced development that allows people to enter one of the most intriguing places in existence—the human mind. Through the use of so-called cognition particles left behind at a crime scene by the perpetrator, detectives from the specialized police squad Kura can manifest a criminal's unconscious mind as a bizarre stream of thoughts in a virtual world. Their task is to explore this psychological plane, called an id well, to reveal the identity of the culprit. Not just anyone can enter the id wells; the prerequisite is that you must have killed someone yourself. Such is the case for former detective Akihito Narihisago, who is known as Sakaido inside the id wells. Once a respected member of the police, tragedy struck, and he soon found himself on the other side of the law. Nevertheless, Narihisago continues to assist Kura in confinement. While his prodigious detective skills still prove useful toward investigations, Narihisago discovers that not everything is as it seems, as behind the seemingly standalone series of murder cases lurks a much more sinister truth.

Mahiro Yasaka is just an ordinary high school student, until one day he is suddenly attacked by a dangerous monster. Just when everything seems to be lost, he is saved by a silver-haired girl named Nyaruko, who claims to be the shape-shifting deity Nyarlathotep from horror author H. P. Lovecraft's Cthulhu Mythos, sent by the Space Defense Agency to Earth. She explains to Mahiro that the creature chasing him was an alien called Nightgaunt, who had planned on abducting and selling him as a slave. After rescuing him from the alien, the Lovecraftian deity falls madly in love with Mahiro and forces herself into his household, much to his chagrin. Moreover, they are soon joined by two others from the fictional universe: Cthuko, a girl obsessed with Nyaruko, and Hasuta, a young boy easily mistaken for a beautiful female. Together, the three eccentric aliens protect Mahiro from the various extraterrestrial dangers that threaten both his and Earth's well-being, all the while making his life a living hell.

After fainting at work, a young lady awakens in the back room of the café she works at with no memory of her life or those around her. Two of her friends, whom she soon learns are named Shin and Toma, are called to help her get home safely. Once she is alone, she meets a spectral boy named Orion that only she can see and hear. He explains that she lost her memories because of his chance visit to her world, so he vows to help her remember who she is. However, regaining her departed memories without worrying those around her may be more difficult than she realizes. In addition to the gloomy Shin and the protective Toma, she must be wary of arousing the suspicions of the captivating Ikki, the quick-witted Kent, and a mysterious man who lurks in the distance. As her amnesia entangles her in the lives of each of these men, her fragmented memories return piece by piece, and the mysteries of her circumstances slowly come to light.

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.