This short movie is a remake of the first half of episode 3 of Ginga Tetsudou 999.

Master assassin Golgo 13 is hired by the advisor of presidential candidate Robert Hardy to assassinate "Queen Bee," the beautiful and deadly leader of a South American guerilla army. Golgo, however, finds this job too easy and digs further information to find out the true connection between Hardy and Queen Bee.

In the year 2062, Earth finds itself fiercely battling Artemis—an AI which rebelled against humankind following a grand-scale workforce automation project failure years prior. In the hope of winning the war, a group of three highly skilled human warriors is assembled, known as the guardians of humanity. Empress, the last surviving guardian, wakes up alone in an empty research facility. Unable to recall anything from the past except a place called "Lighthouse No. 8," she begins to search for answers. It is not long before she discovers an impending threat from Artemis—and she is the sole person who can save the world from destruction.

The characters from previous .hack//G.U. Games and .hack//Roots receive an email from Ovan. He is requesting them to go to Hidden Forbidden Festival where is set up a mysterious summer festival. There they find an AIDA Chim Chim who wishes to peacefully co-exist with the other players of The World. It then transforms into the word "Returner", so they assume it to mean that Ovan will return to The World.