Two years before the events of this manga, the next generation VRMMO, Sword Art Online (SAO) was launched. On its launch day its creator, Kayaba Akihiko trapped 10,000 players inside the game and claimed that if the player died in the game, they would die in the real world.
Among those trapped was Kirito, who found Kayaba's disguise as a comrade in arms and fought with him on the 75th Floor of Aincrad, defeated him and cleared the game.
Two months after finally logging out of SAO, Kirigaya Kazuto decided to have a kendo match with his sister, Kirigaya Suguha, he did not wear protection, but is able to keep up with her. After the practice, he told her that he might take up kendo again, if she would teach him. She considered telling him a secret, but at the last moment she decided not to. As Kazuto left for the hospital, his sister remembered how she discovered that they were cousins rather than siblings while he was trapped in SAO.
In the hospital, Kazuto thought about his beloved, Yuuki Asuna, who was still trapped in the SAO servers with another three hundred players. In Asuna's room he encountered her father, Yuuki Shouzou, and met her fiance, Sugou Nobuyuki. After Shouzou left, Sugou confessed that Asuna hated him, but he could do as he pleased because he had the right due to his department maintaining the server that kept Asuna alive. Kazuto wished to pierce him with a sword when he announced that the ceremony will be held a month later and asked him not to approach Asuna or her family.
Back at home Kazuto was depressed due to his inability to do anything to help Asuna. At that moment, Suguha entered his room and cheered him up before both of them fell asleep on his bed. Kazuto woke Suguha the next morning and she ran away, then he noticed a mail from Agil (Andrew Gilbert Mills), a friend from SAO with a picture of an avatar that resembled Asuna.
At Andrew's restaurant, he told Kazuto about a game called ALfheim Online and its basics, before explaining that the picture was taken from a place in the game. Kazuto noticed that RECT was the company that designed the game and decided to investigate, in order to find out whether Asuna really was trapped within the game.
At home, Suguha was ashamed and in pain because she liked Kazuto, but he cherished Asuna instead. Kazuto entered the game and created his character. Two characters were preparing to fly again, while Kazuto, in his avatar, Kirito, found himself in a forest instead of the starting city of his race.
After logging in, Kirito looked for the Log Out button. Relieved after finding that it existed, he checked his stats and found out that they were the same as his avatar's from SAO. He then looked in his items and found an item called "MHCP001", which he took out and activated. The item transformed into Yui, an AI that he took as his daughter in SAO. She told him that they were in a copy of the SAO's server, thus, his stats data was overwritten, but as long as a human GM did not check it, he would be fine.
Yui transformed into a Navigation Pixie, Kirito told her that Asuna may be in the game and Yui interrupted by notifying about the presence of other players, three were chasing another one. Kirito intervened and beat two players at once while the other decided to leave. Kirito talked to the female player who was being chased and Yui popped out, so Kirito had to invent excuses.
The player presented herself as Leafa and took Kirito to Swilvane, where she explained the game basics and talked about the World Tree. Kirito stood and decided to go to the World Tree while Leafa decided to accompany him. They decided to meet up at a tavern the next day and Logged Out for the night. When Leafa logged out, in the real world she was revealed to be Suguha, who was trying to decide whether to tell Kazuto about her playing ALO.
On her way back to her house, Suguha was remembering why she started playing ALO, when she was interrupted by Nagata, who asked her if she had planned to leave the party. She replied affirmatively and then left. At her house she entered ALO and found that Kirito was shopping and bought a huge sword. After reuniting, Leafa took Kirito to the Tower of Winds, where they met Sigurd, and after an argument they left. Recon managed to reach them before they took off and said that he had found something interesting, so he was staying. He gave some words to Kirito but was cut off by Leafa before Leafa and Kirito departed.
In a cage, Asuna was talking to Sugou, who held her captive. He presented himself as the King of the Fairies Oberon and Asuna as Titania. After scaring her, he declared that the game was just a facade for an experiment in looking for a way to control the human brain. He revealed that he took three hundred players from SAO and they were experimenting on them. Asuna argued back, but Sugou just threatened her before leaving.
After Kirito and Leafa defeated some monsters, Leafa told him off for his style being too reckless for battle, as he would be shot down by magic if they encountered a player party. After some time of flying, a big mountain, which they could not fly over, entered their sight. Leafa told Kirito about the tunnel passing through the mountain and that there was a neutral town in the middle of the tunnel. Since both still had time, Leafa suggested taking turns to log out for a short break while the other protected their lifeless avatar. Suguha ate a sandwich, left one for Kazuto and took a bath before returning. When Kirito logged out, Leafa talked to Yui about love, but they stopped when Kirito suddenly returned. Kirito suddenly felt as if they were being watched and Leafa informed him about tracers, but since Yui could not detect anyone, they decided to continue.
Back in the cage Oberon was teasing Asuna, but she endured it because she realized that she needed free movement. Just before leaving, Oberon told her that he had met Kirito in her hospital room, telling her this with the intent of breaking her will, but instead he accidentally gave her hope and motivated her to memorize the number sequence to open the cage's door.
Meanwhile, Leafa and Kirito finally reached the cave. Leafa notified Kirito that it was called the Legrue Corridor because of the mining town at it's center, Legrue. With Yui's assistance, Kirito activated his night vision magic, which helped them see in the darkness. After 2 hours of navigating the cave and battling with orcs, Leafa suddenly received a message from Recon, warning her to be careful. Just then, Yui sensed 12 players coming their way. Although Leafa attempted to use concealment magic to hide from them, after realizing that they were followed by Salamanders with a high-level tracer, she immediately destroyed the tracer and urged Kirito to run towards the town.
As they were about to reach the gate to the city, the Salamanders blocked off the path to the city with an earth wall spell. As they could not destroy the wall with physical attacks, nor retreat via the lake due to a lake monster, they were left with no alternative but to fight the incoming Salamanders.
- In the light novel, Nobuyuki's wedding was supposed to be a week after talking to Kazuto, while in the Manga it was going to be a month later, like it was in the web version of the novel.
- Kazuto's feelings were expressed much stronger and darker in this manga than they were in the novel, anime, or even the web novel.
- Kirito's first attempt at Voluntary Flight, as well as crashing into the Tower of Wind, is omitted.
- In the light novel, Leafa logged in to ALO before Kirito and she did some potion shopping before he arrived. Later, Kirito and Leafa went shopping together to get new equipment for him.