As an expression of gratitude for the heroes of both the .hack//Sign and the .hack game series, Helba has prepared a special event for all the characters to find the newly established Twilight Hot Springs. The characters can get their well-deserved rest and relaxation by having a soak in the wonderful hot springs, but there is only one problem—the hot springs are hidden, and there have been mysterious player murders. With the only clue being the word GIFT, the race has begun to find the culprit and the location of the hot springs.

Hacka Dolls are AI that scan a person in order to tailor news recommendations and information to their users. These widespread, personalized robots have served many citizens, from government officials to professional sports players. A severe drop in quality leads to the production of three substandard Hacka Dolls. Due to their personality defects, they are sent to Earth, tasked with advancing humanity in whatever way they can. Whether it be encouraging a fujoshi to sell a doujinshi at Comiket or performing in an idol group, the three dolls will complete any task as long as it abides by their moral compass. Despite their shortcomings, they take their mission very seriously and always try their best to assist everyone with incredible enthusiasm.

In 1945, World War II is at its peak. As Japanese cities are fire-bombed and the nation is cornered by US forces, Japan is collapsing under the immense pressure. Gen Nakaoka, a bold, free-spirited young boy, lives in Hiroshima. Struggling with wartime scarcity and barely making ends meet, Gen and his family are hopeful that the conflict will soon end with Japan's imminent defeat and their city unscathed. However, unbeknownst to them, their fate is already sealed with the impending dropping of Little Boy, the US atomic bomb set to cause the devastating cataclysm that will forever change Japanese society.

Tobias, Mary, and Sakuya challenge the impregnable The One Sin, but they lose their way in the maze and unintentionally trap other guild members. A mysterious cat is watching their blunder. Is it another player character or NPC?