The Soul Translator is a state-of-the-art full-dive 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 Sword Art Online survivor Kazuto Kirigaya. He works there as a part-time employee to test the system's capabilities in the Underworld: the fantastical 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 mentioned in reality. 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.

The story is set a couple of years after the events of Sword Art Online, where Kazuto Kirito Kirigaya and his sister Suguha meet up with Asuna Yuuki, Rika Lisbeth Shinozaki, and Keiko Silica Ayano at the SAO Survivor School. Kirito then attends emergency counseling, while the girls go for a swim at the pool. It turns out that said emergency counseling is a subterfuge set up by Seijirou Kikuoka, aiming to rehash the incident of Sword Art Online in hopes of determining Akihiko Kayaba's motives. What will the girls get up to in the pool, and what awaits Kirito and his counseling?

Excelling socially and academically, Asuna Yuuki is on track to ace her high school entrance exams. Her friend and classmate, Misumi Mito Tozawa, advises her to take a short break from studying and join her on the launch day of Sword Art Online (SAO)—the highly anticipated online virtual reality multiplayer game. Asuna accepts her offer and soon meets her in the game. In a cruel twist of fate, Asuna, Mito, and every other player logged into SAO find themselves trapped in the game permanently. The only way out is to clear all one hundred floors of the game, and to make matters worse, dying inside the game will kill the player in real life. With SAO now turned into a nightmare death trap, Asuna and other gamers—such as the lone swordsman Kazuto Kirito Kirigaya—must adapt and survive, all whilst attempting to beat the unforgiving competition to the top.