For thousands of years after its development, mankind used the written word for communication between people and generations. As millenia passed and technology became more prevalent, writing - and thus, communication as a whole - diminished, until it could only be found on cell phones and computer screens. Seeing an opportunity, the sorcerer Sogan Kenzaki starts infecting words with the Nesta Virus, which brings them to life and turns them into monsters called MJBK (Menace of Japanese with Biological Kinetic energy). To counter this attack against humanity, an organization known as DEAVA (Division of EArth Verbalism Ability) assembles a group of youths with the ability of "Verbalism". They have to pilot the vector machines, which are used to form the mechas dubbed "Aquarions". The one wild card in the situation is the self-dubbed "savior", a young man who is the direct relative of a famous calligrapher, named Akira Kaibuki.

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. [Written by MAL Rewrite]

A young wavemaster, only known by the alias of Tsukasa, wakes up in an MMORPG called The World, with slight amnesia. He does not know what he has previously done before he woke up. In The World, the Crimson Knights suspects him of being a hacker, as he was seen accompanying a tweaked character in the form of a cat. Unable to log out from the game, he wanders around looking for answers, avoiding the knights and other players he meets along the way. As Tsukasa explores The World, he stumbles upon a magical item that takes the form of a "guardian," which promises him protection from all harm. Subaru, the leader of the Crimson Knights, along with several other players who became acquainted with Tsukasa, set out to investigate why Tsukasa is unable to log out, and attempt to get to the bottom of the problem before it gets out of hand. [Written by MAL Rewrite]

As a young boy from a noble family in Amawakuni, Arata has always expected to make life his own—until word of the princess growing weak reaches his city. Unbeknown to him, his grandmother had claimed him to be female at birth, and now, with no other girls to succeed the princess from the matriarchal Hime clan, he is next in line for the throne! Disguised as a woman awaiting a replacement to be found, Arata witnesses an assassination attempt on the princess by none other than her own guard, the 12 Shinsho. The crime is pinned on his head, forcing Arata to escape to the Kando forest, where it is said that no one comes out the same. Meanwhile, in modern-day Japan, Arata Hinohara longs for escape from the cruelty of his classmates. Hearing his name called from an alley, he wanders from his path and unwittingly switches universes with Arata from Amawakuni. With his own power as a newly awakened "Sho"—a warrior able to wield Hayagami, weapons with the power of the gods—and the help of his companions he meets along his journey, Hinohara sets out to restore order to this new world. [Written by MAL Rewrite]