Set in a fictional MMORPG called The World, the series follows twins Shugo and Rena. After winning a contest, Rena is given a pair of chibi avatars in the design of the legendary .hackers, Kite and BlackRose. After an odd occurrence, a mysterious AI named Aura gives Shugo the Twilight Bracelet, an item that both aids and hinders him. Rena and Shugo embark on an adventure to find Aura and unravel the mystery of the Twilight Bracelet.
Along the way, Shugo and Rena befriend Mireille, a rare item hunter; the fierce Ouka,;[notes 1] and Hotaru, a peaceful girl. While waiting for an event to start, they encounter a strange girl named Zefie, who is lured to Shugo because she believes the bracelet smells like her mother, Aura. It is later realized that Zefie is a vagrant AI – an AI that acts independently outside the parameters of the game. Zefie’s presence upsets many, including the Cobalt Knights, a group of administrators that follow the rule “If you can’t control it, delete it” to an extreme.
Meanwhile, Balmung, another administrator in The World, encounters problems of his own. The suits, CC Corp’s upper tier executives, are displeased with what little action Balmung has taken against Shugo and his illegal item, the Twilight Bracelet. Balmung’s administrative duties are revoked.
Kamui, the leader of the Cobalt Knights, begins her pursuit of Shugo and company. She captures Shugo and his friends, but allows Mireille, Ouka, and Hotaru to leave after they promise they will not interfere with the workings of The World. Shugo, Rena, and Zefie are left in a cell together. Rena and Shugo disagree over whether to stay until the end. After they come to an agreement to stay and fight, Zefie opens the door to the cell, freeing them.
In the outside world, Ouka, Hotaru, and Mireille decide to return to The World and help Shugo. Kazu, a friend of Balmung, meets up with Shugo and party, carrying “Helba’s Key,” the key to an area called the Net Slums. Kamui shows up, demanding the key to the Net Slums with her knights in tow. Shugo and Kamui face off, which results in Kamui breaking her axe. Zefie tells her that everyone in The World is blessed. Shugo activates Helba’s key and transports himself, Rena, Mireille, Hotaru, and Zefie to the Net Slums. Once at the Net Slums, the party is confronted by Balmung, refuses to allow the party to proceed to Aura unless Shugo can damage him. Shugo struggles, but manages to strike Balmung. Pleased, Balmung hands Shugo the virus cores he’ll need to see Aura; he also explains that only three people can go see Aura. Hotaru and Mireille say their goodbyes to Zefie, Shugo, and Rena as they activate the virus cores and meet Aura. The manga ends with Zefie being reunited with her mother, and Shugo telling Aura of his adventures in The World’.’