In the year 2026, the Augma is released to the public as successor to the Amusphere full-dive system due to its function to simulate reality while the player is conscious (augmented reality). One of the most prominent combat-based games is Ordinal Scale, in which a player's abilities are ranked on a numbered list.

Asuna, Lisbeth and Silica encourage Kirito to play OS upon hearing that Aincrad bosses have appeared. Kirito joins Asuna and Klein in a boss fight where the game's mascot, idol singer AI Yuna, appears and gives players buff effects as she sings. Kirito fails to achieve anything due to lack of physical strength and quickness. Eiji, the number-two player, aides the group in defeating the boss. Before Asuna makes the killing blow, Eiji whispers the word "Switch," a game mechanic from SAO that she recognizes.

The next night, Asuna joins Klein and his group for another boss fight while waiting for their last group member, unaware that he was injured by Eiji the night before. Asuna proceeds to the fight which is again presided over by Yuna. Klein and his group are ambushed and defeated by the sudden appearance of another boss and Eiji. The following morning, as Kirito practices with OS in a park, a girl in a white hood appears and points off into the distance before disappearing. Kirito meets with Asuna, who theorizes that Eiji was a member of the Knights of the Blood Oath named Nautilus, while Yui deduces that the spawning of the Aincrad bosses line up with the SAO dungeon maps.

Asuna, Lisbeth and Silica enter another fight where Yuna and Eiji appear again. Asuna saves Silica when Eiji pushes her into the boss's path but is hit by the boss and passes out. Asuna realizes her memories of SAO are fading and learn that, at a hospital visit with Kirito, the Augma scanned her brain for SAO memories and that it could also happen to other SAO survivors playing OS. Kirito investigates the issue with Sinon for a boss battle, where an SAO player is defeated and a glowing orb floats upward into an OS drone. Yui fails to retrieve it after being locked out by the game. Later, Kirito meets the hooded girl again who repeats her actions from before. Kirito and Yui discover she is pointing towards Touto Technical University.

Kirito goes to the school and meets Professor Tetsuhiro Shigemura who developed Augma, but Shigemura refuses to answer any questions. Before leaving, Kirito notices on Shigemura's desk a picture of a girl who resembles Yuna. Kirito discusses the issue with Kikuoka Seijirou, who informs that Shigemura's daughter, Yuna, died in SAO. Visiting Asuna's home, Kirito makes a promise to her to get her memories back. Kirito encounters the hooded girl again, revealed to be Yuna. When she tells him his rank is too low, Kirito decides on solo-killing as many bosses as he can with aide from Sinon and Leafa.

Days later, the OS players gather at a large concert stadium where Yuna will perform. In the lower levels, Kirito meets with Eiji who claims he has a way to return Asuna's memories. Kirito wins the duel before Eiji reveals that Shigemura has been harvesting memories of SAO players in an attempt to reconstruct his lost daughter's soul and download her as an AI, and having all players in the concert would make removing memories easier. However, the drones used for harvesting possess enough power to damage the players' brains, killing them like the NerveGear did in SAO.

As a horde of Aincrad bosses raid the arena, Kirito and Yuna join the battle. Yuna tells Kirito that the Augma has a hidden full-dive feature and he can use it to defeat SAO's 100th floor boss to end the battle. Before diving, Kirito gives Asuna an engagement ring. Entering the Ruby Palace of Floor 100, Kirito, Lisbeth, Silica, Agil and Sinon confront the boss. They are easily defeated until Asuna, Leafa, Klein and several others from ALO and GGO come to their aid. Yui restores their saved abilities from SAO, allowing everyone to defeat the boss. The voice of Akihiko Kayaba congratulates them on their victory and gives Kirito an extremely powerful sword as a reward.

The group returns to the arena still in full-dive where Kirito, now OS's top-ranked player, dispatches the bosses with his new sword as Kikuoka finds Shigemura in the server room of Argus (the defunct company that ran SAO) and arrests him. The hooded Yuna restores the survivors' memories and fades out of existence since she was coded from the Floor 100 boss. Afterwards, Kirito and Asuna fulfill their promise they made to each other in Aincrad and watch a meteor shower together. Asuna returns Kirito's engagement ring so to properly put it on her hand, which he does.

In a post-credits scene, Kikuoka, who was impressed with Shigemura's attempt at AI and soul reconstruction, recruits Shigemura to Rath.