Despite the defeat of Quinella—the pontifex of the Axiom Church—things have not seemed to calm down yet. Upon contacting the real world, Kazuto "Kirito" Kirigaya finds out that the Ocean Turtle—a mega-float controlled by Rath—was raided. Due to a sudden short-circuit caused by the raiders, Kirito's fluctlight is damaged, leaving him comatose. Feeling insecure about the people at the Axiom Church, Alice brings the unconscious Kirito back to their hometown—Rulid Village, disregarding her banishment due to an unabsolved crime. Now, Alice is living an ordinary and peaceful life close by the village, wishing for Kirito to wake up.
However, tragedy strikes when Alice notices that the Dark Territory has already started to invade the Human Empire. Reassuming her previous alias, Alice Synthesis Thirty, she promises to defeat the Dark Territory in order to defend the world that Kirito and Eugeo worked so hard to protect.
Six months have passed since the fierce battle against Administrator. Alice has brought Kirito to her childhood home, Rulid Village, where they live peacefully. Gazing out at the world that she saved with Kirito, Alice reflects on all that’s happened.
A force from the Dark Territory is attacking Rulid Village. Though she’d lost her purpose in battle, in order to fight for her family, and for the people that Kirito and Eugeo tried to protect, Alice takes up the Osmanthus Blade once again!
The mysterious group that attacked the Ocean Turtle turns out to be a secret unit under orders from the U.S. National Security Agency. And its leader, Gabriel, has battled Kirito and Sinon before.
Shasta, commander of the Dark Territory's dark knights, had intended to use Administrator's death as a chance for peace with the Human Empire. But his plans are thwarted by Emperor Vecta's return to the land of darkness.
Resolved to fight for humankind, Alice joins the forces of the Human Empire, bringing Kirito with her. But while the forces of darkness boast overwhelming numbers, only thirteen Integrity Knights are available to fight for the Human Empire.
The Final Load Test has begun, and the Eastern Gate has collapsed. Incited by Gabriel, now Emperor Vecta, the massive army of the land of darkness pushes on towards the Human Empire.
Integrity Knight Renly Synthesis Twenty-Seven, in battle for the first time, flees his position, allowing goblins from the forces of darkness to infiltrate to the tent where Kirito is.
The powerful formal art unleashed by the Integrity Knight Alice inflicts severe casualties on the forces of darkness. Alice encounters an enemy survivor and learns that Emperor Vecta's objective is to find the "Priestess of Light."
Upon seeing Alice, Gabriel orders his entire army to capture her. The pugilists guild races ahead of the main force. As Alice and Bercouli try to come up with a strategy to counter them, the silent Integrity Knight Sheyta Synthesis Twelve steps forward.
Asuna has logged into the Underworld using the superuser account of Stacia, the Goddess of Creation. After she descends, she is reunited with Kirito, thanks to Ronie and Tiese. But soon Alice arrives, leading to a precarious situation!
Asuna has created a bottomless chasm. The dark knights and the pugilists attempt to cross over to the other side, where the Human Empire Army waits. Meanwhile, Critter releases an announcement about a limited-time beta test for a bizarre new VRMMO.
Due to Gabriel's scheme, U.S. players were given black knight accounts, and are now continuously logging in to the Underworld. They begin mercilessly slaughtering soldiers from both the Human Empire Army and the Dark Territory Army.
Sinon has logged in with the super-account of Solus, the Sun Goddess and rescues Asuna and the others at the last minute. Meanwhile, Leafa logs in with the super-account of Terraria, the Earth Goddess, and descends to the Underworld.
Despite its modest size, the Human Empire Army and Asuna valiantly battle the wave of American players surging towards them. But they’re hopelessly outnumbered, and the Human Empire soldiers start to fall one after another.
Bercouli pursues Vecta, who’s abducted Alice. After a long, vicious battle, Bercouli unleashes his secret sword skill, Uragiri, and finally defeats Vecta, despite having sustained severe injuries himself.
The traitor inside Rath turns out to be a researcher named Yanai. When Higa attempts to restore Kirito, Yanai tries to thwart the operation by holding him at gunpoint. Meanwhile, in the Underworld, Sinon confronts Gabriel, who has logged back in.
Asuna and the others succumb to Vassago and the Chinese/Korean players. Discovering the catatonic Kirito, Vassago kicks his wheelchair over. Enraged, Klein lunges at Vassago, only to be pinned down by enemy players. Just then, someone unexpected appears.
Sinon manages to severely damage Gabriel, but her strength has been sapped. Leafa collapses after wiping out the American players. And Asuna, her situation now hopeless, gazes at Kirito. But the Black Swordsman continues to wander through his dreams.
Escaping his nightmares, Kirito regains consciousness at last. With the Night-Sky Blade in his right hand and the broken Blue Rose Sword in his left, he faces off against Vassago, armed with the Mate-Chopper, now enormous in size.
Alice and Asuna head to the World’s End Altar as Kirito confronts Gabriel. Unless he can defeat Gabriel and return to the real world before the maximum-acceleration phase begins, Kirito will have to spend the next 200 years in the Underworld.
The maximum-acceleration phase has begun. Alice successfully logs out of the Underworld, but Kirito doesn’t make it in time. In the real world, Higa and Kikuoka rush to shut down the STL, in order to disable the maximum-acceleration phase, but…
The “Rath Attack Incident,” masterminded by the American National Security Agency, is over. Now head of the newly formed Oceanic Resource Exploration & Research Institution, Rinko unveils Alice to the world as an authentic artificial general intelligence.
Rinko informs Kazuto that Alice is missing. He’s about to rush to the Rath Roppongi branch when the doorbell rings. In a panic, Kazuto throws open the door, only to find a deliveryman there with a huge cardboard box.