January 2118. Chief Inspector of the Criminal Investigation Department, Akane Tsunemori, receives a report of an incident on a foreign vessel – the body of Professor Milicia Stronskaya has been discovered. Behind the incident is a group known as the Peacebreakers, a foreign paramilitary organization and a new outside threat who are targeting the professor's research papers known as the "Stronskaya Document". Reunited with Shinya Kogami, a former fugitive from the Criminal Investigation Department, Akane grapples with a case that quickly escalates beyond their expectations. The Stronskaya Papers could reveal a truth that would shake Japan's government, and even the Sibyl System, to the core. It is in this untold story that the missing link is revealed.

Specials included in the BD/DVD release of .

After vanquishing another boss and stepping through the gates of the fifth floor, the misfit duo Kazuto "Kirito" Kirigaya and Asuna Yuuki are greeted with a beautiful landscape of crumbling ruins and catacombs steeped in mystery. This idyllic adventure is short-lived, however. Tensions between the Dragon’s Knights Brigade and the Aincrad Liberation Squad—the two leading guilds focused on clearing Sword Art Online—continue to rise and threaten the fragile stability of the frontline raiding group. Kirito and Asuna are forced to act quickly, making a desperate gamble and gathering a small number of allies for a dangerous mission. As a result, Asuna and Misumi "Mito" Tozawa must come to terms with their relationship after the near-tragedy that forced them apart on the first floor.

During summer break, Tetsuo asks Sakie to join him on patrol duty for the local summer festival, which both the demis and Himari and her friends go to. As each group decides to check out a nearby shrine, they get spooked by some strange occurrences, which turn out to be each other. As the next term begins, Tetsuo converses with an invisible woman named Matsuri.