.hack//Sign follows the story about Tsukasa being mind-trapped into the game. Despite being a “fantasy quest type adventure”, it does not rely on action sequences. Instead, the show is driven by mystery, slowly revealing its secrets to the viewer while paying much attention to the individual characters. Questions like what happened to Tsukasa in the real world, who he really is and why he is unable to log out are driving points of the story.
Soon after the beginning of the series Tsukasa is led to a hidden area. There he meets Morganna, depicted as a voice without physical appearance, and Aura, who appears as a young girl clad entirely in white, floating asleep above a bed. The storyline introduces Morganna as an ally, but her real intentions are unknown at this point.
As the story progresses many characters are introduced, some who want to help, some who have ulterior motives. Then more questions arise as to “what is happening in the game itself, who are these various characters, what are their true goals and what will happen to Tsukasa”. All the while he is seen struggling with his increasingly dire situation as well as his own social and emotional shortcomings. Tsukasa isolates himself, but eventually he begins to get closer to other players, and builds strong relationships with some of them; the most important is the one born between him and Subaru, a kind and thoughtful female Heavy Axeman.
In the meantime, the anime follows the quest for the Key of the Twilight (黄昏の鍵 Tasogare no Kagi?), a legendary item rumored to have the ability to bypass the system in The World. Some characters want the Key to gain the power this supposedly confers. Others believe the item will provide Tsukasa with a way to log out. Despite their reasons for seeking it, everyone agrees that it is related to Tsukasa in some way, as he is also a factor bypassing the system in the game. His body being in a coma in the real world adds a sense of urgency to the quest.
Near the end of the series Tsukasa’s real-life identity takes a more central place in the storyline, particularly in relation to his growing bond with Subaru. The series shows his fear and insecurity as he confesses to her that he is probably a girl in the real world. It is also at this point when Tsukasa is told Morganna’s plan by a highly skilled hacker called Helba. Morganna conceived the plan to link Aura to a character who could corrupt her with negative emotional data, placing her in a state where she would never awaken. The chosen character was Tsukasa, as his mind was filled with distressful memories of his real life. Helba also suggests that when Aura is able to awaken, “the Key of the Twilight will take form”.
The story reaches its climax when Tsukasa confronts Morganna. Then the viewer sees him declaring that he is no longer afraid of her or of reality, and will log out because there is someone he wants to see. This statement triggers Aura’s awakening, allowing Tsukasa to log out. The last scenes feature an emotional encounter between Tsukasa’s real-life self, finally shown to be a girl, and the real-life player behind Subaru.