Two years have gone by since Kirito and Eugeo left Rulid Village. In the capital city, Centoria, both boys have attained their goal of being admitted to the North Centoria Imperial Swordcraft Academy.

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 have been rescued by the young girl, Cardinal, who has secluded herself inside the Central Cathedral’s Great Library. Cardinal explains to Kirito how the Axiom Church and the Taboo Index came to be, starting with Administrator’s past.

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.

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.

Carrying the hopes of Cardinal, Eugeo, and Alice in his heart, Kirito stands yet again and visualizes the Black Swordsman, the top player who cleared SAO. For the sake of everyone he’s encountered in this world, Kirito, faces off with Administrator.

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!

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.

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."

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.

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.

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.

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.

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.