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She first meets Twelve and Nine when Twelve helps her escape from a group of mean girls. During a class trip to the Tokyo Metropolitan Government office, she again meets Twelve while he is setting up for the first attack. Twelve gives her an explosive stuffed toy and orders her not to throw it away unless he says so and walks away. While trying to find Twelve again, the bombs inside the building begin detonating after the building is evacuated. Only then, is Lisa called by Twelve and Nine, who give her two options: die or become their accomplice. Lisa replies that she doesn't want to die so Twelve saves her from the burning building. From that point on, Twelve appears to keep tabs on Lisa's whereabouts and meets her at a bookstore without Nine's consent (although Nine later reveals he already knew Twelve's actions).
Lisa runs away from home and meets Twelve at a park who tells her to go home. She refuses, commenting that she's stupid for believing her situation would change for the better by getting involved with the two boys. Lisa leaves and rescued shortly thereafter by Twelve from two security guards. While they ride Twelve's motorcycle to Nine's location, Lisa asks if the boys plan on destroying the world and they laugh, something Lisa reveals she hasn't done in "a really long time." At the apartment, Nine disapproves of Lisa staying with them, but the girl collapses due to fever so he reluctantly allows her to stay until she gets better. While Nine and Twelve discuss Lisa, she awakens and accidentally sets off all the cellphones, including the one that was to be hooked up to their newest bomb. She faints when she finds out that she could have blown up the whole building and upon coming back to her senses, takes a bath. She overhears Nine and Twelve arguing whether she should stay or not and decides to demonstrate her usefulness by trying to prepare a meal, but her plan backfires since she burns it.
Lisa again offers to help them but, Nine shows her pictures of the aftermath of the subway train bombing and states that this is what they were doing, which shocks her. Nine tells her to not get in their way, that's the best thing she could do. Afterwards she goes to the roof and Twelve joins her. Twelve tells Lisa that he suffers from synesthesia, a condition that allows him to see sounds as different colors; he describes her voice as being a "pale yellow" and mentions that it's rare for him to see a voice that color. Although he was trying to cheer her up, Lisa says it would have been better if she wasn't here. Twelve comforts Lisa, knowing she is troubled about Nine's disapproval of her presence and says she shouldn't worry about it. Lisa momentarily stuns Twelve when she mentions that she's a little jealous of Twelve for knowing Nine so well.
Five sends a text containing a riddle to the public: 'GIGFHEEGMHJL FD. Gaius Julius Ceasar gone to Arab. Sphinx.', posing as Sphinx. The answer turns out to be a set of coordinates leading to Haneda Airport's International Terminal. Knowing that they will be caught by Five while trying to enter the terminal, Nine reluctantly decides to bring Lisa along with them, since she isn't known to be associated with him and Twelve.
Nine and Twelve decide to play along with Five's chess game. Later on Lisa also gets something to do in this mission. Twelve
asks Lisa to create a distraction; after some hesitation, she sets off flares that trigger a fire alarm. But afterwards she gets caught by Clarence. They bring her inside a plane with the bomb in it. She calls Nine and Twelve for help describing her and the bomb's whereabouts: a plane that is on autopilot and headed for a terminal filled with numerous commuters. Nine and Twelve manage to rescue Lisa from the plane and the plane explodes without injuring anyone.