In the year 2022, a massive online role-playing game called Sword Art Online (SAO) is launched. With the aid of "NerveGear" technology, players can control their avatars within the game using nothing but their own thoughts. Kazuto Kirigaya is among the lucky few who get their hands on the first shipment. He logs in to find himself, with ten-thousand others, in the scenic and elaborate world of Aincrad. However, in a cruel turn of events, the players soon realize they cannot log out; the game's creator has trapped them in his new world until they complete all one hundred levels of the game. In order to escape Aincrad, Kirito will now have to interact and cooperate with his fellow players. Some are allies, while others are foes. Sword Art Online is not all fun and games: if they die in Aincrad, they die in real life. Kirito must adapt to his new reality, fight for his survival, and hopefully break free from his virtual hell.

A year after escaping Sword Art Online, Kazuto Kirigaya has been settling back into the real world. However, his peace is short-lived as a new incident occurs in a game called Gun Gale Online, where a player by the name of Death Gun appears to be killing people in the real world by shooting them in-game. Approached by officials to assist in investigating the murders, Kazuto assumes his persona of Kirito once again and logs into Gun Gale Online, intent on stopping the killer.

The Soul Translator is a interface which interacts with the user's Fluctlight—the technological equivalent of a human soul—and fundamentally differs from the orthodox method of sending signals to the brain. The private institute Rath aims to perfect their creation by enlisting the aid of Kazuto Kirigaya. He works there as a part-time employee to test the system's capabilities in realm generated by the Soul Translator. As per the confidentiality contract, any memories created by the machine in the virtual world are wiped upon returning to the real world. Kazuto can only vaguely recall a single name, Alice, which provokes a sense of unease. When Kazuto escorts Asuna Yuuki home one evening, they chance upon a familiar foe. Kazuto is mortally wounded in the ensuing fight and loses consciousness. When he comes to, he discovers that he has made a full-dive into the Underworld with seemingly no way to escape. He sets off on a quest, seeking a way back to the physical world once again.

Despite the defeat of Quinella—the pontifex of the Axiom Church—things have not seemed to calm down yet. Upon contacting the real world, Kazuto "Kirito" Kirigaya finds out that the Ocean Turtle—a mega-float controlled by Rath—was raided. Due to a sudden short-circuit caused by the raiders, Kirito's fluctlight is damaged, leaving him comatose. Feeling insecure about the people at the Axiom Church, Alice brings the unconscious Kirito back to their hometown—Rulid Village, disregarding her banishment due to an unabsolved crime. Now, Alice is living an ordinary and peaceful life close by the village, wishing for Kirito to wake up. However, tragedy strikes when Alice notices that the Dark Territory has already started to invade the Human Empire. Reassuming her previous alias, Alice Synthesis Thirty, she promises to defeat the Dark Territory in order to defend the world that Kirito and Eugeo worked so hard to protect.