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.hack//ZERO Vol.1 Phantom Pain is the first and so far only book in the .hack//ZERO novel series.
The storyline of Phantom Pain focuses on a girl named Junka Nimura, who controls a PC in The World named "Carl". Carl enjoys annoying people in The World, and uses methods such as scamming and PKing to ruin the fun of other players. While adventuring by herself Carl visits her favorite area, the Hulle Granz Cathedral. Inside the Cathedral she runs into Sora and becomes infatuated with his attitude. She begins seeing him regularly, but during one of their meetings they are interrupted by Aura. Aura's presence causes Sora to experience extreme pain, so Carl tries to attack Aura in order to defend him. As a method of self-defense Aura temporarily disconnects the Cathedral from the rest of The World, knocking Carl out of the area.
Carl tells her friend Alph about her experience. This causes Alph to visit the Descendants of Fianna Orca and Balmung who are busy investigating strange phenomena within The World. Meanwhile Carl finds herself unable to contact Sora. Desperate for information, she posts about him on the BBS unknowingly drawing the attention of Subaru, the former leader of the Crimson Knights.
Remembering the incident with Tsukasa, Subaru becomes concerned for Carl's safety and agrees to meet with her. During the meeting Subaru attempts to explain why Sora is dangerous, and the incidents surrounding Tsukasa. However, when Subaru mentions Aura Carl grows angry, and storms off in the middle of the conversation.
Worried about Carl's behavior, Alph contacts Sieg and convinces him to talk to her. Unfortunately he is unable to get through to her. Carl confronts Alph about her meddling and the two separate. Depressed, Carl returns to the Cathedral and is surprised to see Sora waiting for her. However Sora doesn't recognize her and begins to attack Carl. Shocked, Carl simply waits to be PKed but is saved by the sudden appearance of Aura. Noticing Aura, Sora turns his attacks towards her and begins using system defying powers like energy beams and teleportation to attack with. To Carl's surprise Aura simply lets Sora hit her. When Carl asks why she's not fighting back, Aura's response is simply "Hurting Sora would make Carl sad". Realizing that Aura is actually a good person, Carl shouts at Sora and is able to temporarily distract him. Finally recognizing Carl, Sora says her name. Happy that he remembered her, but still recognizing the danger she's in Carl grabs Aura and flees the Cathedral.