Within a MMORPG (Massive Multiplayer Online Role-Playing Game) known as "The World", there exists a multitude of players who login, day in and day out, to enjoy the ficticious, but all too real experience of the game. However, with the invention of games that envelope the user by all 5 senses, "special cases" have been noted (but kept from the public). These special cases are when a user locks up in a coma.

The story is about a player named Tsukasa who attempts to logout of the game, but is immediately thrown back in. While walking around, pondering what to do, he meets a girl by the name of Mimiru and briefly asks her if she has ever had trouble logging out. He finds her too "annoying" and then they agree to never see each other again. Mimiru alerts a friend, Bear, of the problem player Tsukasa is having. Bear decides that he will aid Mimiru in her quest to locate Tsukasa and help him as much as he can. Unfortunately, Tsukasa has befriended a "monster" that has capabilities unlike any of the players have seen. In an instant, Tsukasa defeats a member of the renowned Crimson Knights, essentially Moderators of the World under the command of Subaru.

Eventually, Tsukasa is captured by the Crimson Knights and is questioned by Subaru about the monster and a mysterious cat player who appears earlier in the series. After asking Tsukasa these questions (ones which he doesn't really have answers to), he is set free, however, the mystery of Tsukasa and the exact reason as to how he has powers above the level of an Admin is still a mystery.On a side quest, BT and Sora are searching for an item that is apparently linked to Tsukasa and the monster. The item, shrouded in mystery, was mentioned long ago by a "hacker" and expert player on the BBS. The item is known as the "Key of The Twilight".