In the near future, a virtual reality game called Sword Art Online has been released where players control their avatars with their bodies. One day players discover they cannot log out, as the game creator is holding them captive unless they defeat the final boss. However, if they die in the game, they die in real life. Their struggle for survival starts now.
In a flashback, on September 14, 2025, Sinon, who had accidentally fallen down a trap chute while navigating a dungeon below SBC Gurokken in GGO, discovers a boss-class monster and decides to die while trying to defeat it. To her surprise, the position she chose for her attack was out of the monster's attack range, and thus, by conserving her ammo and accurately hitting the boss's weak spot, she is eventually able to defeat it and acquire a new sniper rifle, the PGM Ultima Ratio Hecate II. In the present day, during an ambush on an enemy squadron, Sinon attempts to snipe a target, but he turns out to be a bodyguard named "Behemoth," who overwhelms her squadron with aminigun. When Sinon and Behemoth are the only ones remaining on the battlefield, Sinon manages to shoot Behemoth with her Hecate while falling from the air, earning her victory in the gunfight, despite suffering severe damage to her avatar. Meanwhile, in Alfheim Online, Kirito plans to tell Asuna about something.
After witnessing Kirito's win in his first preliminary match, Death Gun asks Kirito if he is the real deal. Before he can answer Kirito notices his tattoo of Laughing Coffin and wonders if he's run into him before.
At the entrance to Thrymheim, Yui explains that the quest they were given was created by the Cardinal System's Automatic Quest Generation Function and that if they did not succeed in their quest, a final war event, Ragnarok, would be triggered. Sometime later, at the end of the second floor of Thrymheimr, the group encounters two minotaurs, and they are forced to rely on Sword Skills that could deal elemental damage to them in addition to physical damage, but also leave the player rigid for a few seconds after the skill is used up. With Kirito revealing his new technique of using consecutive Sword Skills with each of his swords to avoid the period of rigidity, they are able to defeat the two minotaurs. Later, after defeating the boss guarding the entrance to the lowest floor of the castle, they encounter an NPC woman trapped in an ice cage along the way. Although the others insist that it is a trap and plan to avoid her, Klein ignores their advice and frees the woman, who was revealed to be Freyja. Instead of running away, Freyja asks to join the group and Kirito reluctantly agrees to the request. After preparing for the final battle by recharging their buffs, the group enters the throne room, where they met the king of the frost giants, Thrym.
After hearing that a new update from New Year's Eve opens up floors 21-30 of new Aincrad, Kirito and the others race to reach floor 22 with the hope of once again purchasing the home he shared with Asuna and Yui.
In the season finale, Asuna, Yuuki as well as all of their friends continue to live happily in the world of Alfheim and New Aincrad. From duels and quests to taking bosses head on, the group is determined to make the most of their time together, by any means. However, when Asuna receives urgent news of Yuuki's condition, the line between her two worlds will become thinner than ever. And she will learn how the human spirit, as well as the love which sustains it, transcends all life.
Kirito, along with his childhood friend, Eugeo, has been tasked with cutting down a colossal tree called the Gigas Cedar. They're swinging their ax when their friend Alice arrives with lunch. As they eat, the three friends decide to go to a fabled cave.
Kirito wakes up to find himself inside a mysterious world evoking a fantasy game. His memory fuzzy, he tries to log out, but is unable to return to the real world. After wandering aimlessly, he finds himself underneath a colossal tree.
Kirito makes up his mind to journey to Centoria. Since he'll need Eugeo's help, he also decides to fell the Gigas Cedar. Meanwhile, Alice's little sister, Selka is worried about Eugeo, and opens up to Kirito about her concerns.
Kirito and Eugeo realize Selka has taken off to the End Mountains alone, and decide to chase after her. As they enter the cave, they encounter goblins, presumably from the Dark Territory, and must engage in a battle.
In the real world, Kazuto Kirigaya lies unconscious. At Kikuoka's request, Kazuto is moved to a well-equipped hospital, but when Asuna and Suguha try to visit, they're turned away. Suspicious, Asuna and the others split up to find out more about Rath.
Asuna infiltrates Rath, the research lab in the Ocean Turtle, where she relentlessly grills Kikuoka about Kazuto's whereabouts. Kikuoka reveals that behind the development of the Soul Translator is a mind-blowing objective of epic scale.
Now an Elite Disciple along with Kirito, Eugeo struggles with the question of what he should infuse in his sword so he can become stronger. When he's taunted by First-Seat Elite Disciple Raios and Second-Seat Humbert, Eugeo decides to accept Humbert's request for a duel.
Ronie and Tiese are late getting to the dorm. Kirito rushes out in search of them, but no sooner has he gone than Frenica appears. She tells Eugeo about how she's suffered at Humbert's hands, and that Tiese and Ronie went to confront him about it.
Kirito and Eugeo are now considered criminals for having violated the Taboo Index and are thrown into the underground prison in the Central Cathedral. Meanwhile, on the Ocean Turtle in the real world, Asuna is watching over Kazuto as he's being treated.
Kirito and Eugeo escape from their cell, only to find their way blocked by Eldrie Synthesis Thirty-One, under orders from Alice to lie in wait for them. Kirito and Eugeo struggle against him until Eugeo realizes that he's seen Eldrie somewhere before.
Cardinal finishes her explanation of the Administrators Origins and gives Kirito a word of warning. Then the three discuss plans to free Alice and save the world from the Administrators control. They're going to need some weapons.
After being entrusted with the fate of the world by Cardinal, Kirito and Eugeo head to the top floor of the Central Cathedral. They find their confiscated swords, only to be attacked by the bow-wielding Integrity Knight Deusolbert Synthesis Seven.
Kirito and Eugeo are on their way up the stairs of the Central Cathedral when they encounter two girls named Linel and Fizel. As they stand, wondering what two children are doing there, they let their guard down and.
Though riddled with wounds, Kirito manages to activate his Perfect Weapon Control art. Continuing on their way to the top floor of the Central Cathedral, Kirito and Eugeo find themselves standing before a strange-looking floating platform.
When Kirito and Alice both unleash the Perfect Weapon Control art in the Cloudtop Garden, the impact rips a hole into the seemingly impregnable Central Cathedral wall, which sends them both flying outside.
Eugeo reaches the ninetieth floor of the Central Cathedral, which turns out to be a vast bathing area. The perplexed Eugeo encounters Bercouli Synthesis One soaking in the bath. Meanwhile, Kirito and Alice are still climbing the Central Cathedral wall.
Seeing Alice's reaction when he mentioned the name Selka, Kirito decides to tell her the truth about the Integrity Knights. Meanwhile, after being knocked unconscious during his battle with Bercouli, Eugeo awakes on the top floor of the cathedral.
Kirito and Alice reach the communal bath on the nintieth floor. There, they find the Integrity Knight Commander, Bercouli, who's been turned to stone by Chudelkin. Alice breaks down in tears upon seeing her mentor's tragic plight, but then.
Standing in Kirito and Alice's way is Eugeo, who's undergone the Synthesis Ritual and become an Integrity Knight. Kirito is rattled, until Alice admonishes him into resolving to fight Eugeo with everything he's got.
Cardinal appears on the top floor of Central Cathedral for a showdown with her bitter foe of the last two hundred years. She moves to achieve her objective of deleting Administrator, only to see the fallen sword golem rise up again.
After Cardinal and Eugeo's defeat, Kirito is about to fight the Pontifex before she manages to transform all of the people who live in the Underworld into a great weapon to repel the Dark Territory's invasion and attack the "other side".