The players of a virtual reality MMORPG, Sword Art Online, are trapped and fighting for their very lives. After it is announced that the only way to leave the game is by beating it, Kirito—a very powerful swordsman—and his friends take on a quest to free all the minds trapped in Aincrad.
On November 6, 2022, the VRMMORPG, Sword Art Online (SAO), is officially released, with 10,000 copies released and sold immediately. Kirito, who beta-tested the game, logs-in to the world of Aincrad and meets Klein, a new player, who asks him to teach him the basics of the game including the Sword Skill battle system. Later, after several hours in the game, Kirito and Klein discover that they cannot log out. Shortly after, the pair are teleported to the town square, where they see that all other players have also been transported to the location. A red-hooded Game Master then appears in the sky and reveals himself to the crowd as Akihiko Kayaba, the game's creator. He tells them that he intentionally removed the log-out option. He cautions that they cannot log-out by simply removing the NerveGear, the VR helmet they use to log-in the game, as it will kill them instantly. The only way to log out is for the players to beat and clear all 100 floors of the game. Should they die in the game, their real bodies will perish as well. As a parting gift, Akihiko gives them a mirror that alters their in-game avatars to resemble their real appearance. Kirito asks Klein to follow him to the next town to level up before resources are depleted, but Klein politely declines as he wishes to remain with his friends. Kirito then heads out, vowing to be free from the game. By the end of the first month, 2,000 players have died and the 1st floor has yet to be cleared.
One month since the start of the fun-turned-deadly game, 2,000 players have already died, and the first floor has yet to be cleared. Kirito attends a meeting organized by fellow beta-tester Diabel, who announces to the attendants that his party, a group of characters adventuring together in a role-playing game, has found Illfang the Kobold Lord, the boss of the first floor. Parties are formed, and Kirito teams up with a young girl named Asuna. The next day, Diabel's raid group arrives at the boss' room and battles Illfang and his minions. When Illfang's health becomes low, Diabel goes for the finishing attack. Kirito attempts to warn him, but Illfang attacks down first and mortally wounds Diabel. As he dies, Diabel begs Kirito to defeat the boss and save the players. Though they destroy the boss, Kirito is accused of being a "beater"—a combination of a "beta-tester" and "cheater"—for Diabel's death.
Four months have past with more powerful players and guilds clearing the game's floors. After saving a guild called the "Moonlit Black Cats", a group of friends from the same school club, their leader Keita thanks Kirito and ask him to join their guild and teach the only female in their guild, Sachi, to fight better. Kirito agrees while hiding the fact he is at least Level 40, twice higher than the others as they slowly and safely level up at low-level floors that have been cleared. Kirito bonds with his new friends, especially Sachi, who admits to Kirito she's afraid to die which he assures her he will protect her and they will be free one day. But on June 12, 2023, as Keita goes to buy a house for the guild, against their usual methods and Kirito's advice, the Black Cats decide to earn some money by going to the upper floors where they set off a trap, locking them in a room with higher level Mobs. Kirito desperately tries to save his friends but they are killed one by one until Sachi is the last to fall. Blaming himself over his friends death, including Keita, who committed suicide upon learning what happen, Kirito goes on a suicidal quest upon learning a rumor there is a way to revive the dead. On December 24, 2023, Argo the informant reveals to Kirito the location of a special boss named Nicholas the Renegade who has an item that can revive the dead. As Kirito heads there, he is followed by Klein and his guild, who fears for his safety. They are soon surrounded by the Holy Dragon Alliance guild who are also after the item. As Klein and his guild hold off the Holy Dragons, Kirito faces against Nicholas alone. But much to his distraught, Kirito discovers the item can only revive the dead within ten seconds after their deaths. To Kirito's surprise, he receives a recorded message from Sachi. Sent to him on Christmas Eve in the event of her death, Sachi tells Kirito not to blame himself over her death and that he should continue living to be free from the game. As she ends the message by humming "Rudolph the Red-Nosed Reindeer" before saying goodbye, Kirito sadly cries.
On February 23, 2024, a beast tamer named Silica, quits a party after arguing with their leader, Rosalia. Silicia is ambushed by monsters whilst making her way alone through the forest and her dragon familiar, Pina, is killed trying to protect her. As Kirito saves her, he tells Silica of an item at the Hill of Memories on the 47th floor that can revive her familiar within three days after it's death, offering to accompany her there. As they spend time together, Kirito warns Silicia of "orange players", players who attack other players and "red players", players who kill other players and someone is eavesdropping on their plans. As they make their way towards the Hill of Memories the next day, Kirito tells Silica about his younger sister who is actually his cousin, who she reminds him of. As they finally retrieve the item, the Pneuma Flower, they are confronted by Rosalia and her men, who are actually part of the Titan's Hand, a notorious orange player guild and are after Silica's flower. However, Kirito reveals part of his reason for escorting Silica was to draw Rosalia out to arrest her. The guild realizes Kirito is the infamous Beater "The Black Swordsman", and due to his higher levels and advanced skills, he outmatches Rosalia and her men, forcing them to surrender and send them to prison. As Kirito prepares to return to the front lines, he makes a promise to Silica that they'll meet again in the real world as she revives Pina.
During a meeting between guilds and players on March 6, 2024 on the 56th floor, Asuna, who has now become Vice Commander of the Knights of Blood Oath guild, propose a plan to lure a boss they are fighting into a village but is opposed by Kirito, as the NPC villagers will be killed. A month later on the 59th floor, Kirito is taking a nap until Asuna arrives, criticizing him for being lazy but he convinces her to relax as well. To thank him for guarding her while she was asleep, Asuna decided to buy lunch for him at a town on the 57th floor. However, they discovered a player killed, hanging outside the church, impaled with a spear. As they both investigate, Kirito wonders how the player was killed in a safezone unless he was dueled by another player or someone has found an exploit to kill players. Yoruko, a girl who was a friend of the victim, Kains, saw someone behind Kains before he was hanged. Asuna and Kirito heads towards Egil's shop to help them find clues on the murder weapon, which Egil learns it's a custom made weapon by a player named Grimrock. Explaining what they discovered to Yoruko, she reveals how she and Kains are related to Grimrock. Six months ago, she, Kains and Grimrock were part of a eight-man guild called the Golden Apple lead by Griselda, Grimrock's ingame wife. One day the guild acquired a rare ring and voted whether to use it or sell it, with three members, Yoruko, Kains and Schmit, now a member of the Holy Dragon Alliance, voting to use it. Griselda went out to sell the ring but was killed. Yoruko believes the killer is targeting the three of them as he suspect they were involved in Griselda's death. After getting Schmit and explaining to him everything, Yoruko becomes paranoid, believing Griselda's ghost wants revenge against them. But Yoruko is killed after someone throws a dagger from outside.
Kirito chases after the assassin but he manages to teleport away. Kirito is still unsure how it was possible to kill someone in a safezone which a paranoid Schmit thinks Griselda's ghost is really after him. After accidentally seeing a dropped sandwich vanishing and talking with Asuna about the game's marriage system which allows both couples to share each others inventory, Kirito finally figures out how Yoruko and Kains "died" and who is Griselda's killer. It turns out Yoruko and Kains are still alive and tricked people into thinking they were dead by using damaged armor that will eventually disappear along with teleport crystals at the same time to make it look like they died. Yoruko and Kains confront Schmit at Griselda's grave as they are investigating who Griselda's killer is. After Schmit explains he had no part in Griselda's death, the three of them are surrounded by the notorious player-killing guild, the Laughing Coffins, who have come to kill them. They are soon rescued by the timely arrival of Kirito, which the Laughing Coffins retreat and Asuna arrives with the man who hired them and Griselda's killer, Grimrock. Grimrock reveals he killed Griselda, who was also his wife in the real world, because he couldn't accept his kind, dutiful wife he loved now became a fearless, independent leader. Asuna shoots back on Grimrock for killing Griselda, telling him he didn't love his wife but was just obsessed with her. After Yoruko, Kains and Schmit take Grimrock into custody, Kirito and Asuna talks about marriage and how he would still love his partner after seeing a different side of her, they see Griselda's ghost, who thanks them.
On June 24, 2024 at Lindas on 48th floor, Asuna visits her friend the blacksmith Lisbeth or "Liz" at her smith shop before going adventuring, and Liz suspects she's going with a boy she likes. Later, Kirito arrives at Liz's shop as he's looking for a custom-made sword to buy. Much to Liz's shock, Kirito's sword Elucidator easily breaks her strongest sword. Angry and her pride hurt, Liz convinces Kirirto to let her join him to the Western Mountain on the 55th floor to get a rare mineral from a dragon that eats crystals so she can use the mineral to make a stronger sword. As they arrive at the Western Mountain, Kirito advises Liz to hide as he fights the dragon. However, she ignores his advice when she comes out when she thinks the dragon is almost defeated. The dragon blows her into a deep pit and Kirito jumps in to save her. While they both survive, they can't get out of the pit and are forced to sleep there for the night. Liz asks Kirito to hold her hand while they sleep, which brings her to realize that she can feel another person's warmth even though they are just data. She also realizes that she has feelings for him. The next morning, Kirito discovers that the mineral they are seeking, a Crystallite Ingot, is under the snow as the hole is the dragon's nest. The dragon returns and Kirito grabs Liz with him as he stabs the dragon's back, forcing it to carry them out of the hole before jumping out. Now safe with the mineral, Liz manages to create a new sword for Kirito, Dark Repulsor. As she asks Kirito to use her as his exclusive smith and is about to confess to him, a worried Asuna arrives. Realizing Kirito is the boy Asuna likes, Liz excuses herself from them. As Liz cries over her heartbreak, Kirito finds her and tries to comfort her. Accepting her predicament, Liz promises to help Kirito as his smith if he promises to win the game and free them all.
After adventuring on the 74th floor, Kirito finds a Ragout Rabbit, a rare animal with top grade meat. Since he can't cook well, Kirito decides to sell it to Egil. When Asuna arrives and tells them she has mastered her cooking skills, Kirito decides to give the meat to Asuna in exchange they both eat it together. But Kuradeel, Asuna's escort sent by the Knights of Blood, is against Asuna inviting Kirito to her home as he is a Beater but Asuna ignores him. As they arrive at her home at Selmburg on the 61st floor, Asuna cooks the rabbit meat for dinner. As they talk, Asuna and Kirito discuss how two years have past since they were trapped in the game and many players seems to accept living in Aincard with less then five hundred players clearing the floors. Both agree to party up and explore the dungeons at the 74th floor. However, Kuradeel was following Asuna to prevent her from meeting up with Kirito. To settle things, Kirito has a duel with Kuradeel where if he wins, Kuradeel will leave Asuna alone. Kirito wins the duel by breaking Kuradeel's sword. Kuradeel refuses to give up but Asuna relieves him of his duties and orders him to return to Knights of the Blood Oath headquarters to await punishment. As Kirito and Asuna explores the 74th floor dungeons, they discover the boss room and its boss, The Gleam Eyes.
Kirito and Asuna flee from the boss and take a break for a snack when they meet Klein and the Furinkazan guild. The army also appears, visibly exausted from exploring the floor. They demand Kirito to give them the map he made of the floor, and despite Asuna and Klein's protests he willingly complains with their request. Kirito, Asuna and Klein keep exploring the floor, clearing the monsters there, just to learn that the army is confronting the boss by themselves despite Kirito's warnings, and to make matters worse, the teleport crystals do not work in the boss room. As the members of the army are killed one by one, they launch themselves against the boss to protect the survivors and Kirito is forced to deploy a special skill of his he used to keep in secret that allows him to fight with two weapons, one in each hand, defeating the boss with a series of quick strikes. After the fight, Kirito collapses with HP almost totally depleted, just to wake up instants later, seeing Asuna in tears, who asks him to form a party with him, to which he agrees. Some time later, Kirito and Asuna are brought before Heathcliff, commander of the Knights of Blood who challenges him to a duel. If Kirito wins, Asuna is allowed to leave the guild and join his side, but he must join the guild instead should he loses. Kirito agrees to the terms and accepts Heathcliff's challenge.
The duel between Kirito and Heathcliff is held at an arena where a large crowd has gathered. Asuna warns Kirito to be careful about fighting Heathcliff as he has an unique skill called Divine Blade which gives him maximum strength and defense. Heathcliff at first is able to overpower Kirito but the tides turn when Kirito forces Heathcliff on the defensive. Just as Kirito is about to deal the winning strike, Heathcliff mysteriously manages to dodge it and defeats Kirito. Now a member of the Knights of Blood, Kirito is asked by Asuna why he never join guilds and he reveals what happened to his old guild. Asuna comforts Kirito and tells him she will protect him. Later, Kirito is asked by fellow member Godfrey to follow him and a seemingly remorseful Kuradeel to the 55th floor dungeons for a skill assessment. As they take a lunch break, Kirito notices too late that the water he and Godfrey drank contains a paralysis effect. Kuradeel reveals he is a member of the Laughing Coffins and how he plans to kill both Godfrey and Kirito while making it look like they were killed in an ambush. After he finishes off Godfrey, Kuradeel attempts to kill Kirito but is saved from certain death by the arrival of Asuna who tracked them on her map. Asuna quickly decimates Kuradeel's health until critical stages. Kuradeel begs Asuna for forgiveness which is a ruse. When Kuradeel's is about to attack Asuna, Kirito jumps in between them, blocking the attack with his arm before killing him. Asuna feels guilty for what happened but Kirito calms her by kissing her, telling her how much he cares about her and wants to protect her. They agree to a take break from adventuring and stay at her home for the night. Later, as he sits next to Asuna at her bed, Kirito tells of a place they can be alone together and proposes to her, which she happily accepts.
Kirito and Asuna take a break at their new home in a secluded village in the 22th floor. As the two of them spend time together, they find a lost girl in the forest. To their curiosity, the girl doesn't have a cursor above her, suggesting a glitch. After taking the girl to their home, she wakes up and claims not to remember anything but her name Yui. Yui, unable to pronounce Asuna's and Kirito's name right, calls them "mama" and "papa" respectively. Believing she got lost from her family, Kirito and Asuna decide to head to the Town of Beginnings on the 1st floor to find Yui's relatives and regain her memories before they go back to the front lines. Instead, they find a young woman named Sasha and the children she's taking care of being harassed by the Army for taxes. Asuna attacks their leader until he and the rest of his men run away. As Sasha and the children thank Asuna, Yui tells Kirito she realizes she has never been to the Town of Beginnings before. A mysterious static sound affects everyone before Yui faints.
Kirito, Asuna and Yui are resting at Sasha's church where she takes care of the younger children until Yulier of the Army arrives. Yulier explains the Army under their leader Thinker had good intentions of helping players but as the Army got bigger, people like Kibaou started abusing power on others. Thinker was going to expel Kibaou over the Gleam Eyes incident but the latter trapped him at a secret dungeon on the 1st floor which is why she has come to Kirito and Asuna for help. With Yui refusing to stay at the church, Kirito, Asuna and Yulier reluctantly bring her alone to rescue Thinker. When they arrive at his location, a boss called "The Fatal Scythe" attacks them. Kirito and Asuna orders Yulier to escape together with Thinker and Yui as they fight the boss but it is too strong. As the boss is about attack Kirito, Yui confronts the boss, who is unable to damage her due to being an "Immortal Object" and defeat the boss. Yui, finally remembering her past, reveals to Kirito and Asuna that she is an AI counselor created by the game's Cardinal system whose purpose was to monitor and counsel the players on their mental state. But on the day of game's launch, Cardinal refuse to allow to her interact with the players which she was forced to watch their mental state deteriorating until she learned about Asuna and Kirito and wanted to meet them. Despite the revelation, Asuna and Kirito still accepts Yui as their daughter but she tells them goodbye as she's going to be deleted for interfering in the game. Refusing to accept it, Kirito uses the GM console Yui left behind to save Yui by turning her into a crystal item. With Yui's data save on his NerveGear local memory, Kirito and Asuna hopes to recreate her in the real world.
While fishing near a lake, Kirito encounters Nishida, an old man and a network security manager who oversaw the game's development. Nishida claims that despite honing his fishing skill, he is unable to create delicious dishes with it. Kirito then invites him to his home for Asuna to cook the fish he just caught for them. During their meal, Nishida mentions a huge fish he tried to catch many times but failed and asks Kirito to help him. Nishida manages to hook the fish and gives the rod to Kirito to pull it away. The fish is revealed to be a huge monster whom Asuna slays. Soon after, Kirito receives a message from Heathcliff and, upon meeting him, they learn that a scouting party was trapped and killed in the 75th level's boss room, thus a team of players from several guilds is being assembled to confront it. As the time for the battle approaches, Kirito asks Asuna to stay behind fearing for her safety, but Asuna refuses, claiming that she'd rather die than live without him. She also mentions that all players' real bodies must be currently being treated in hospitals and their condition cannot be kept indefinetly, thus fleeing to live by themselves inside the game is out of question. As the players enter the boss room, they are confronted with "The Skull Reaper", a powerful monster capable of killing players with one blow. Kirito, Asuna and Heathcliff confront the creature head on while the other players attack it from the sides.
After the group defeats the Skull Reaper, suffering 14 casualties in the battle, Kirito deduces that Heathcliff is, in fact, Akihiko Kayaba himself. Akihiko paralyses everyone except Kirito, and then offers Kirito the chance to face him in a one-on-one duel where, should Kirito win, Akihiko would log out all the remaining players. After giving his best wishes to the others, Kirito accepts the challenge but is unable to overcome Akihiko's absolute defense and intimate understanding of the game's mechanics. As Akihiko readies the finishing blow, Asuna overcomes her paralysis and takes the hit instead, losing all her HP and disappearing as a result. Distraught by Asuna's death, Kirito loses the will to fight and receives a fatal stab from Akihiko. However, at the point of death, Kirito remembers Asuna's belief in him and manages to regain enough substance to defeat Akihiko using Asuna's sword. They are both killed simultaneously and the game is declared cleared on November 7, 2024. Kirito then awakens high above the game world, where he finds both Asuna and Akihiko. Akihiko informs Kirito and Asuna that he has logged out all the other players as promised, and also explains his motives for creating Sword Art Online before disappearing. Kirito and Asuna then tell one another their true names, Kazuto Kirigaya and Asuna Yūki, and embrace each other as the world falls apart. To his surprise, Kazuto awakens in a hospital in the real world and, despite being physically weak, sets off to search for the real Asuna.
Even two months after he had been logged out of SAO, Kazuto continues to be plagued with nightmares about Asuna. It is also revealed that throughout his two-year coma in the game, his younger cousin, Suguha, has been constantly worrying about him. The pair have a kendo spar, and though Kazuto loses, Suguha is both shocked and curious about his unusual yet proficient sword fighting skills -- a result of his time in SAO. Later, Kazuto goes to the hospital to visit Asuna who, along with 300 other players, has yet to wake up even after the SAO incident. It is there that he meets an associate of Asuna's father, Noboyuki Sugou, who reveals to Kazuto that he intends to be adopted into Asuna's family while she is still comatose as a precursor to marriage, much to Kazuto's fury. Claiming this as his right since that it was his company that had been keeping Asuna alive after SAO's developer went bankrupt, he informs Kazuto that the ceremony will occur in a week and tells him not to see her again. Later at home, Kazuto breaks down before Suguha, who tells him not to give up, despite harboring her own feelings for him. The next morning, Kazuto receives an e-mail from Egil with a screenshot of an avatar resembling Asuna from another game.
Kazuto visits Egil, who explains that the photo he sent came from ALfheim Online, an MMO where players take the role of fairies capable of flight. He goes on to explain that the figure resembling Asuna was spotted somewhere on the game's World Tree. Noticing Sugou's company is behind the game, Kazuto decides to once again don his Nervegear and take up his role as Kirito in ALfheim Online. Upon selecting his character race as a Spriggan and diving in, he enters a strange warphole which leads him to a forest, where he finds to his surprise that his stats are identical to his SAO avatar's. He also discovers that he still has the SAO in-game item containing Yui's data, which he activates to bring Yui into ALfheim as a Navigation Pixie. Yui deduces that the game is made using a copy of SAO's servers, which was why all common skills and stats from SAO had been carried over to Kirito's ALfheim avatar. As Kirito gets used to his flight controls, a couple of players named Lyfa and Recon are seen fighting against some enemies. As Recon is defeated and Lyfa is outnumbered, Kirito crash lands before her and steps in to help defeat the assailants.
Lyfa thanks Kirito for saving her and teaches him how to fly properly. They then travel to the Sylph Territory (Sylvein) where they meet one of Lyfa's party members, Recon. Lyfa and Kirito go to an inn and have a conversation about how Kirito can get to the top of the World Tree. Seeing Kirito's determination to reach the top of the tree, Lyfa decides to help him and asks him to meet her at the inn the next day. When Lyfa logs out, it is shown that she is actually Suguha. Meanwhile, Asuna is seen in a gigantic bird cage at the World Tree, held by the game master, Oberon the Fairy King. She recognizes Oberon as Sugou, who insists on calling her "Titania". He reveals to Asuna how he captured the minds of 300 players before they were logged out from SAO including her own, as part of his research on memory control. He threatens to alter Asuna's memories if she does not cooperate with him and then departs, leaving Asuna in despair and quietly begging for Kirito to save her.
After recalling how she got into VR gaming, Suguha meets up with Recon's real life persona, Shin'ichi Nagata, informing him that she will be quitting their party to join Kirito. Logging in once more as Lyfa, she accompanies Kirito in shopping for new equipment, having a run in with her old party, led by Sigurd who doesn't take kindly to Lyfa's departure. Before Kirito and Lyfa set off, Recon approaches them, saying he will continue to observe Sigurd's party due to some suspicions he has about them. Meanwhile, as Asuna learns from Sugou that Kirito is still alive, she takes keen observation of the keycode for her cage's lock. As Kirito and Lyfa reach a safe landing point, where they will have to continue on foot through some caves to reach the World Tree, they take turns logging out to refresh themselves, with Lyfa getting a brief chat with Yui. After Kirito returns, they both set off again, unaware that they are being followed by a mysterious group.
While passing through a cave, Leafa receives a message from Recon cautioning her to take care. She and Kirito then realize that they are being followed and try to escape, only to be cornered by a large group of Salamander players. Kirito asks Leafa to support him with her magic while he fights the group by himself. However, he is unable to break their formation until Yui comes up with a plan to have Leafa cast some protective magic on Kirito, while he conjures a spell that temporarily transforms him into a giant demon. In his new form, Kirito obliterates his enemies, but spares one whom Kirito bribes in exchange for information. The Salamander player reveals that his party was ordered to attack Kirito and Leafa by the same group which attacked them during their first encounter. After arriving at the next town, Suguha logs out for a while and answers a phone call from Shin'ichi. Shin'ichi tells her that Sigurd is in cahoots with the Salamanders, who plan on attacking the Sylphs and Cait Siths during a meeting to establish an alliance. Upon returning to the game, Leafa explains the situation to Kirito and states that it would be in his best interest to continue without her, as allying with the Salamanders may be the best option for him in order to reach the top of the World Tree. Kirito instead chooses to help her and makes use of his speed to break out of the cave with her.
Kirito and Leafa reach the place of the meeting just as the Salamanders prepare to attack the Sylphs and Cait Siths. Seeing that they have no chance against them, Leafa thanks Kirito for all he has done for her and asks him to continue to the tree by himself, but he rushes forward and stands before the Salamander General Eugene instead, bluffing that he is a messenger for the Spriggans and Undines and to attack them would lead to the four factions waging war against the Salamanders. Eugene does not believe him and challenges him to a duel claiming that he may trust his word should he manage to hold himself for thirty seconds. Kirito is severely punished by Eugene's sword which can bypass his defenses, until he conjures a huge smokescreen, making use of it to steal Leafa's sword and turn the tides of the battle fighting Eugene with two swords. After Eugene is defeated, he is revived by Sakuya and leaves in peace with his army. Having his treason exposed, Sigurd is contacted by Sakuya who strips him of his title and has him banished from the Sylph territory. After learning that the now allied Sylphs and Cait Siths plan an incursion to the World Tree in a couple of days, Kirito donates a large sum of money to aid in their war effort and departs ahead with Leafa. Meanwhile, Asuna makes use of the code she had previously learned to open the cage and escape.
Kirito and Leafa reach Arun, the capital of Alfheim, located directly beneath the world tree. However a sudden announcement of an emergency shutdown for server maintenance prompt the two to find a nearby inn and log out. The next day, Suguha accompanies Kirito to visit Asuna at the hospital. Meanwhile, in the World Tree, Asuna stumbles upon a room where experiments are being made with the brains of the other SAO players trapped in ALO. She then attempts to log out of the game by using the GM console inside the room, but is captured by two of Sugou's assistants. However, she manages to snatch a key card before being thrown back to her cell. Back in the real world, Suguha gets heartbroken upon seeing Kazuto tending to Asuna, and is comforted by Kirito after she logs back as Leafa on ALO, still unaware that both him and her brother are the same person. Later as the pair approach the World Tree, Yui suddenly detects Asuna's presence, prompting Kirito to fly ahead leaving Leafa behind.
Leafa tries to stop kirito as he dashes for the lower branches of the world tree only to be stopped by the new barrier that had been "patched" into the game earlier. Kirito then finds a card that is dropped down by Asuna due to hearing Yui calling to her "Momma!". Kirito then has Yui identify the card as a Sys-Admin pass code card for use on a GM console, and makes a mad dash for the opening gate to the world tree quest. Kirito makes a heroic fight to reach the portal at the top of the chamber, but is diced to bits before reaching it. Kirito dies from the hundreds of spawned "Guardians", but is saved by Leafa. Upon being revived by Leafa, Kirito states he can not stop fighting until Asuna is safe, which at that time Leafa learns that Kirito-Kun is actually her brother in real life. Or so it seems, as in the real world after they both logoff that they are not actually blood related brother and sister.
Kazuto recalls when he was ten, he learn he was not related with Suguha, leading him to become detached from his family and become engrossed in online gaming. But due the lessons he learn during his time in SAO, he decides to make amends with his family. Wanting to sort things out, Kazuto asks Suguha to meet him in ALfheim. As Leafa contemplates whether she should stop seeing Kirito in-game anymore, she runs into Recon, whose unsuccessful attempt to confess to her cheers her up. Leafa then challenges Kirito to a one-on-one fight, during which they both end up throwing the duel and apologize to each other. After Kirito explains he won't be able to say what he thinks of Suguha until Asuna is rescued, Leafa agrees to help him in his quest, dragging Recon along with her. Kirito once again takes on the guardians, this time with assistance from Leafa and Recon. As the number of guardians keep increasing, Recon uses a self-destruct spell to create a gap for Kirito to get through, but it is filled up all too soon. Just as things look dire, Sakuya and Alicia arrive with their armies to back them up. Using Leafa's sword, Kirito manages to break through the guardians and reach the top, only to find a moderator-locked door in his way. Using the card Asuna gave them, Yui manages to open the door, teleporting her and Kirito to a new location.
Arriving at the top of the World Tree, Kirito and Yui finally manage to reunite with Asuna. However, they are suddenly hit by high gravity magic, which forces Yui to retreat, and are confronted by Sugou. As Sugou reveals his plans to control the human soul, he chains Asuna up and starts to molest her in front of Kirito, who is stabbed and forced to endure incredible pain. As Kirito falls into despair, he hears the voice of Akihiko, who encourages him to stand up and fight, realising the pain is nothing compared to the pain of SAO. Using Akihiko's administrative abilities, Kirito manages to strip Sugou of his high level and challenges him to a fight with no pain absorption, showing him what true pain is before finishing him off. After logging Asuna out, returning her to the real world, Kirito meets with the remnant of Akahiko's memory, who gives him an item called The Seed before leaving. After returning to the real world and giving his thanks to Suguha, Kazuto makes his way to the hospital to finally meet Asuna for real.
Rushing to the hospital Kazuto is attacked by an injured Sugou with a knife at the parking area. Kazuto manages to disarm him, and after considering everything Sugou has done, Kazuto spares his life. Kazuto finally meets with Asuna where they have a tearful reunion. On May 16, 2025, Kazuto and Asuna have returned to school, attending a special school for students who were trapped in SAO. As they have lunch, Kazuto reveals Sugou was arrested by the police after their fight and the crimes he committed were exposed by one of his employees. The 300 players that were trapped by Sugou were freed but his experiments shocked the public. Due to the scandal, Asuna's father and his higher ups resigned and shut down Alfheim Online with other VRMMORPG following suit. Later, Asuna, Kazuto and Suguha heads to Agil's bar along with Liz, Silica, Yoruko, Kains, Sasha, Yulier, Thinker, Klein and his guild where they have a party to celebrate Kazuto for freeing them from SAO. Kazuto gives Agil "The Seed" to be analyzed which is revealed to be a program that allows anyone with a server to create their own VRMMORPG and transfer players to other VRMMORPG easily. "The Seed" is uploaded to the internet which revives the VRMMORPG genre. Later that night in Alfheim Online, now run by a new company, Kirito meets up with Leafa where they share a dance in the sky. Leafa decides to leave since she feels she cannot keep up with her brother but Kirito reveals his character stats have been reset. As a surprise, the floating castle Aincrad from SAO has been brought into Alfheim Online which Kirito then declares he intends to finish clearing all 100 floors. With their friends from SAO and Alfheim Online flying towards the castle, Leafa, Kirito, Asuna and Yui join them.