Breakup is the twelfth episode of .hack//Roots.
Meanwhile, in the Serpent of Lore, Yata and Pi examine Ovan's PC-Body. Yata remarks that most of it is relatively normal, but that Ovan's left arm contains a large amount of data, and is heavily encrypted. Pi wonders if they have the capabilities to open it, but Yata reassures her that "there is no box that cannot be opened."
In Mac Anu, Haseo discusses Ovan's disappearance with Phyllo. He tells Phyllo that he's beginning to think that Ovan won't be returning to "The World." He admits that he's been feeling lost ever since Ovan vanished, as if he'd lost his purpose. Phyllo chides him about playing the game for Ovan, and suggests that Haseo start playing for the people that are still around. Elsewhere, in the Twilight Brigade's @HOME Sakisaka tells Tabby that he's decided to quit the Guild. He explains that with Ovan disappearing, and Shino admitting that the Key of the Twilight doesn't exist anymore that there's no reason to remain in the Guild. Rather than spend time in a Guild without a purpose, he intends to spend his time in "The World" having fun. Tabby seems confused by this, saying that with or without a goal, she still finds the Twilight Brigade fun.
Back in the city, Haseo finishes his conversation with Phyllo. As he turns to leave he is approached by B set, who has also come to speak with Phyllo. She tells Haseo that Shino is probably in a lot of pain right now, and that she's counting on him to support her. Taking her advice to heart Haseo goes to visit Shino at the Arche Koeln Waterfall. After a few awkward questions about her wellbeing, Shino decides to open up to him and admits that she's concerned about the state of the Twilight Brigade, especially regarding Sakisaka. Though Haseo says he isn't that concerned about Sakisaka, he surprises Shino by offering to talk to him. Smiling at him, Shino graciously accepts Haseo's help.
On Mac Anu's bridge, B set begins her conversation with Phyllo. She tells him that her only reason for remaining in "The World" was because Ovan was there. And now that he's vanished, she's also lost her motivation to play. She announces that she intends to quit the game. She admits that her only regret, was that she was unable to see Ovan one last time. Phyllo says that he won't try to stop her, since it'd be pointless to try and change something she'd already decided. Meanwhile, in the Twilight Brigade's @HOME, Haseo and Shino meet with Tabby and Sakisaka. Haseo says that he'd like to continue searching for the Key of the Twilight, but is surprised when Shino says that it'd be a bad idea. Sakisaka tells him that unless he could find real evidence that the Key exists, searching for it would be pointless. He says that in the early days of the Brigade they used to do crazy things like search every inch of a field, or spend hours in the Lost Grounds in the hopes of finding the Key. Not wanting to repeat that kind of experience, Sakisaka shoots down Haseo's idea as well. Tabby suggests searching for Ovan instead, but Sakisaka throws that out for similar reasons, saying that if Ovan wanted to be found he'd have already revealed himself to the Brigade.
Out in the city, Sakisaka talks to Tabby about her idea. He asks how she intended to search for Ovan anyway. When Tabby says that she's worried about Ovan's safety Sakisaka reminds her that Ovan is an adult, and is fully capable of taking care of himself. To his surprise Tabby gets angry at this and storms off. Back in the Brigade's @HOME Shino asks Haseo why he made his suggestion. He says that he believed that the Twilight Brigade would reunite if they had a common goal again, but that he realizes his idea was a stupid one. He decides to take a walk, unaware that his desire to help the Brigade has touched Shino.
In the Serpent of Lore, Yata begins to scan Ovan's left arm. As the scan approaches the lock on his arm it begins to shake, as is something was trapped inside of it. Ovan begins pleading for Yata to stop.
Back in the @HOME Shino is surprised to see B set enter. B set tells her that she's about to quit, but that she wanted to talk to Shino one last time. She asks Shino about her feelings for Haseo, and tells her that she should depend on him instead of Ovan. Shino says that that would be impossible, since Ovan is a very special person to her. B set seems amused by this, and tells her that even now, she can't beat her. Waving goodbye she leaves the @HOME. Meanwhile Tabby returns to the dungeon where Shino obtained her rare Cat Claws. Clearing the dungeon by herself she kneels down in front of the Beast Statue and begins to cry, unsure of what she should do next. Standing in the Coite-Bodher Battlefield Haseo is going through a similar situation.
Inside the Hulle Granz Cathedral Shino talks with Phyllo. She tells him about all the people who have recently quit the game, and that she feels differently from them. When Phyllo questions her about it, Shino says that she intends to stay in "The World" until it is destroyed. Phyllo wonders if that's because of Ovan, and admits that he never should have introduced her to him. Shino tells him that she has never regretted meeting Ovan, then asks to be left alone for awhile. She tells Phyllo that if it has to be broken, then she intends to break it herself, although she never specifies exactly what "it" is. Phyllo seems to understand this statement, and leaves the Cathedral.
Inside the Brigade's @HOME, Sakisaka notices that Shino is missing. When he asks Haseo about it, Haseo tells him that Phyllo recently sent an e-mail saying that Shino wouldn't be accessing for awhile. Sakisaka gets angry about this, and tells Haseo that it's proof of a connection between Ovan, Shino, and TaN. He speculates that Ovan obtained the Key of the Twilight for himself, and is now sharing it with TaN. Shino, who was part of the plot has now left to join them. Haseo is unimpressed by Sakisaka's rant, but when he is unable to give an adequate explanation for Ovan and Shino's disappearance Sakisaka gets even angrier. Throwing away his Guild Key, Sakisaka announces that he's quitting the Brigade and storms out. Tabby is upset by this, and Haseo asks her if she intends to leave with him.
Meanwhile the scan of Ovan's arm continues. Suddenly the seal on his arm breaks, and Ovan's body is enveloped in a dazzling white light. In the @HOME Haseo suddenly looks up, Tabby asks if he received a mail from Shino, but Haseo says that's not it, he just though he'd heard somebody calling. Tabby asks if it was his parents, but Haseo tells her that would be impossible, since he lives by himself. Changing the subject she asks him if he knows how to contact Shino in real life. Haseo tells her he doesn't, but that she'd probably give him her contact information if he asked. Looking at their situation, he says he probably should have asked earlier. Tabby tells him that he's been getting pretty close with Shino recently, and grows annoyed when he answers evasively. She tells Haseo that he's never looked at her the way he looks at Shino, and that she always feels alone. He reminds her that she's always hanging out with Sakisaka, but she tells him that she'd rather spend time with him. Angry, Tabby tells Haseo that he just wants to stick her with Sakisaka, so he can be alone with Shino. She storms out of the @HOME, leaving a confused Haseo behind. Suddenly Haseo receives a flash mail, which causes him to jump out of his seat.
Near the fountain in Mac Anu's Market District Tabby finds Sakisaka. She tells him that she's going to quit the Brigade too, since it's more fun with him. Sakisaka is confused by her sudden change of heart, but agrees to let her follow him. The two go off on an adventure, while Phyllo looks down at them with an unreadable expression.
Traveling to the Hulle Granz Cathedreal, Haseo sees Shino inside. As he approaches he notices that her PC Body has changed, her old white outfit has been replaced with a black one. Seeing his puzzled expression Shino tells him that it's an expression of her devotion. She then disbands the Twilight Brigade and tells him that she won't vanish from "The World" like Aura did. She says that she intends to wait for Ovan alone until he reappears. Haseo tells her that she won't be alone, he'll wait with her. Though surprised at his comment, Shino smiles and thanks him.