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. (Source: ANN)

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.

While playing the newly released MMORPG "The World," Minase Mai and Tomonari Kasumi collapse in the real world and are sent to the hospital after hearing a mysterious sound. Only Mai recovers, while her friend Kasumi slips into a mysterious coma. Mai is later approached by the creator of "The World," Tokuoka Junichiro, who unveils to her that, just like her friend, six other players across the country also collapsed while playing "The World" and are now in mysterious comas. What exactly is "The World," what is this mysterious sound Mai keeps on hearing, and why are people slipping into comas from this game? Minase, Junichiro, and their acquaintances set off to get to the bottom of this problem before any further harm happens.

After the termination of the incredibly popular virtual reality MMORPG "The World," a new version of the game—The World R:2—is brought online. On his first day in the game, newcomer Haseo thinks he has made some friends to quest with. However, as if mocking his sentiments, they kill his character just for fun. Luckily, he is saved by a mysterious, one-armed player named Ovan who offers to show him around The World. Alongside Ovan and his cleric friend Shino, Haseo enjoys a wonderful first year in the game. But this peaceful life is shattered when Shino's character is killed by a familiar figure notoriously known as Tri-Edge, whose victims have all fallen into comas in the real world. In a fit of rage, Haseo vows to find the elusive Tri-Edge and kill him. Taking place during Haseo's first year in The World, .hack//Roots explores the friendships Haseo built in the game before Tri-Edge ripped them away.