In the first volume of the .hack//Liminality series, a Japanese school girl Mai Minase and her friend Tomonari Kasumi became unconscious from playing an online computer game and was rushed to the hospital. Fortunately, Mai Minase regained consciousness, but Tomonari remains in a comatose state. Later after the incident, Mai is one day on her way to school until she ran into a man named Junichiro Tokuoka who claims to know what caused her friend Tomonari to be in a coma. At that time, Mai doesn't know or believes him. Later, Mai had no choice but to believe Tokuoka and tries to find out how the popular online game, "The World" did this to Tomonari. Can Mai and Tokuoka find out clues about "The World" and wake Tomonari Kasumi up out of his coma?

Several weeks after the meeting in Hida-Takayama on Christmas Eve, Junichiro Tokuoka, Kyoko Tohno, Yuki Aihara, and Mai Minase all gather on a dinner boat in Tokyo Bay, to prepare for their risky (and most certainly illegal) mission. Despite their nervousness, each one is dedicated to helping Ichiro Sato complete the mission sent from Helba. Ichiro himself soon arrives on a different boat. While traveling to their destination, Ichiro reveals the true nature of the problems that have been plaguing The World. Harald Hoerwick's program, Fragment, had been nothing more than a program to create an "Ultimate AI". The system to create this A.I. had somehow become self autonomous, and was working to delay the birth of the A.I. known as Aura, to keep itself from finishing its purpose and ceasing to exist. If the problems are to be solved, the Ultimate A.I. must be born, and it's up to Tokuoka and his team to help that event occur.