Set four years after the .hack games, the manga follows the adventures of a pair of twins--Rena and Shugo. The story takes place in the a fictional MMORPG called The World. After winning a contest, Rena is in possession of a pair of chibi avatars in the design of the legendary .hackers known as Kite and Black Rose. After an odd occurrence, Aura appears and gives Shugo the Twilight Bracelet. Shugo embarks on an adventure to find Aura and unravel the mystery of the Twilight Bracelet, An item that both aids and hinders those involved with it. Along the way, Shugo and Rena meet many friends including Mireille the rare hunter, the fierce Ouka, and the peaceful Hotaru. One night, while waiting for an event to start, Shugo and friends encounter a strange girl named Zefie. Zefie 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 of the parameters of the game. Zefie's presence upsets many including the Cobalt Knights, a group of administrators that follows 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 the little action Balmung has taken against Shugo and his illegal item, the Twilight Bracelet. Balmung's administrative duties are revoked and he is fired. Kamui, the leader of the Cobalt Knights, begins her pursuit of Shugo and company. She successfully captures Shugo and friends, but allows Mireille, Ouka, and Hotaru to leave having them promise they will not interfere with the workings of The World. Shugo, Rena, and Zefie are left alone in a cell together. Rena believes it is worthless to fight any longer and wants to give up. Shugo disagrees saying they should stay until the end. After they come to an agreement to stay and fight, Zefie, much to the amazement of Shugo and Rena, opens the door to the cell and frees them. On the outside world, Ouka, Hotaru, and Mireille decide their fate. With a little help from Mistral, all three agree to return to The World and help Shugo. Kazu, a friend of Balmung, meets up with Shugo and party with a mysterious item called "Helba's Key", the key to the net slums. Kamui shows up, demanding the key to the net slums with her knights in tow. Shugo and Kamui finally face off ending in Kamui breaking her ax. 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 who claims he will not allow the party to proceed to Aura unless Shugo can damage him. Shugo struggles, but then applies everything he learned in The World and manages to strike Balmung. Balmung is pleased and hands Shugo the virus cores he'll need to see Aura. He also explains that only three people can go and everyone else must stay behind. 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, Aura, and Shugo telling Aura of his adventures in The World.

AKA Legend of the Twilight