The series focuses on a Wavemaster (magic user) named Tsukasa, a player character of a virtual-reality massively multiplayer online role-playing game (MMORPG) called The World. Tsukasa wakes up to find himself in a dungeon in The World, but he has no recent recollections as he wonders where he is and how he got there. The situation gets worse when he discovers he is not able to log out and is trapped in the game. From then on, along with other players Tsukasa embarks on a quest to figure out the truth behind his abnormal situation.

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.

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".
In the meantime, the anime follows the quest for the Key of the Twilight, 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 the 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.

.hack//SIGN (pronounced dot-hack-sign) is a prequel to the .hack video game and OAV series. The TV series was created with the specific goal of explaining the back story to the game and OAV series.

01 Role Play
02 Guardian
03 Folklore
04 Wanted
05 Captures
06 Encounter
07 Reason
08 Promise
09 Epitaph
10 Compensation
11 Party
12 Entanglement
13 Twilight Eye
14 Castle
15 Evidence
16 Depth
17 Conflict
18 Declaration
19 Recollection
20 Tempest
21 Despair
22 Phantom
23 The Eve
24 Net Slum
25 Catastrophe
26 Return