In the year 2022, the Virtual reality Massive Multiplayer Online Role-Playing Game (VRMMORPG), Sword Art Online (SAO), is released. With the Nerve Gear, a virtual reality Helmet that stimulates the user's five senses via their brain, players can experience and control their in-game characters with their minds.

On November 6, 2022, all the players log in for the first time, and subsequently discover that they are unable to log out. They are then informed by Kayaba Akihiko, the creator of SAO, that if they wish to be free and log out of the game, they must reach the 100th floor of the game's tower and defeat the final boss. However, if their avatars die in-game, their bodies will also die in the real world. The story follows Kirito, a skilled player who is determined to beat the game. As the game progresses, Kirito eventually befriends a female player called Asuna who becomes his partner and lover. After the duo discover the identity of Kayaba's avatar in SAO, they confront and defeat him, freeing themselves and the other players from the game.

Upon returning to the real world, Kirito learns that Asuna and a small group of SAO players are trapped in another VRMMORPG called Alfheim Online (ALO). Their imprisonment in ALO is part of a plan devised by Nobuyuki Sugō to subdue Asuna and marry her, in an attempt to take over her family's company. Helped by old friends from SAO along with new allies, Kirito stops Nobuyuki's plans and finally reunites with Asuna in the real world.

Soon after, Kirito plays another VRMMORPG called Gun Gale Online (GGO) to investigate the mysterious connection between the game and deaths occurring in the real world. He eventually discovers that the culprits are former members of a murderous guild he has previously encountered in SAO.

After solving the murders in GGO, Kirito is recruited to assist in the development of a state-of-the-art game, UnderWorld (UW), which has an interface that is far more realistic and complex than that of the previous games he had played. In UW, the flow of time proceeds thousands of times faster than in the real world. However, Kirito ends up falling for a trap and wakes up inside the game, unable to log out and he starts looking for a way back to reality.