An unnamed atheist Japanese salaryman, in the moment of being murdered by a disgruntled subordinate who he had fired due to poor performance at work, is confronted by an entity that declares itself to be God who condemns the salaryman for not having 'faith'. The salaryman disbelieves in its existence, criticises its various statements from his perspective as an atheist and mockingly terms it as 'Being X'. The entity decides to reincarnate the salaryman into a world where he would face sufficiently difficult circumstances to turn to Being X for help.

Fifteen years ago, a hyperspace gate appeared in the middle of the Pacific Ocean, connecting Earth to a strange world filled with fairies and monsters. The city of San-Teresa became a home for over two million of these otherworldly visitors. The city of San-Teresa became a home for over two million of these otherworldly visitors. Unfortunately, the population boom also brought its fair share of problems—drugs, prostitution, and trafficking. To combat the rampant crime lurking in the city's shadows, a new department was established in the San-Teresa Metropolitan Police.

The story begins when Yggdrasil, a popular online game is quietly shut down one day. However, the protagonist Momonga decides to not log out until the end. Momonga is then transformed into the image of a skeleton as "the most powerful wizard." The world continues to change, with non-player characters (NPCs) beginning to have personalities. Having no parents, friends, or place in society, this ordinary young man Momonga then strives to take over the new world the game has become.

Why are we here? Why are we doing this?
Before Haruhiro had realized what happened, he was surrounded by darkness. Why was he here? Where was here? Even now, he still didn't know. Those around him were the same as him, no one remembered anything other than their own names. And when they emerged from the darkness, the world that awaited them seemed like something out of a video game.

This is a story, a "ghostory" of sorts, about scars that bond, monsters that haunt, and fakes that deceive.
The story of Koyomi Araragi begins through a fateful encounter with the all-powerful, blonde-haired, "hot-blooded, iron-blooded and cold-blooded" vampire, later introduced as Shinobu Oshino. Their tragic rendezvous results in the end of Araragi's life as a human and his subsequent rebirth as a vampire—a monster. However, this encounter is only the start of his meddlings with the supernatural. Koyomi's noble personality ultimately sees him getting further involved in the lives of others with supernatural afflictions.