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- While Twelve goes to rescue Lisa, Nine leaves to retrieve the plutonium. Meanwhile, Shibazaki and Hamura visit Souta Aoki, the former welfare minister, to question him about the Athena Project. Surprisingly, Aoki tells them everything about it: its connection to the members of the Rising Peace Academy, the experiments on the gifted children within the "Settlement," and the use of drugs to produce the Savant syndrome artificially. Aoki says that Five was the only child to have survived the project. However, two other children, Nine and Twelve, managed to escape. He tells Shibazaki that the mastermind behind the project was Dr. Shunzo Mamiya, the politician behind Shibazaki's demotion. While Nine constructs the final bomb, Twelve reaches the amusement park and finds Lisa handcuffed on a Ferris wheel. Her body is laced with several bombs, and a timer activates when the ride begins to move. Twelve comforts her and begins disarming the bombs individually, although they both realize he cannot defuse them all in time. Twelve refuses to leave Lisa and reluctantly tells Five the location of the plutonium in exchange for stopping the timer. Five cuts the power to the Ferris wheel, trapping Twelve and Lisa midair. Five reveals that she knows they stole a prototype atomic bomb rather than plutonium. The Metropolitan Police Department raid the school where Nine has just retrieved the bomb. Five orders him captured alive before she suddenly collapses. (en)
- The media broadcasts that the foiled airport attack is the work of Sphinx. The officers who accompanied Shibazaki to Haneda Airport are suspended for three months by their boss, while Shibazaki is permanently suspended. Shibazaki learns from his daughter Haruka, a physics student, that a person could construct an atomic bomb from plutonium. Meanwhile, Five tracks down Lisa at the Sphinx hideout and sends a bomb, but Lisa escapes before it detonates. Nine, Twelve, and Lisa flee to an abandoned video arcade where Nine states that Lisa is a liability. Shibazaki continues his investigation and, while at the National Archives, he discovers that a decade ago, the Rising Peace Academy implemented an operation called the Athena Project. He visits Ichiro Fujiwaka, a politician who was involved, and threatens to expose his son's illegal activities. Fujiwaka reveals that orphaned children were gathered and tested, and those gifted with Savant syndrome were selected for the Athena Project. Suspended officer, Hamura, joins Shibazaki, and they continue their investigation. Feeling guilty, Lisa leaves Nine and Twelve, only to be captured by Five's allies in the FBI. Later, Twelve receives a threatening text message from Five, revealing that Lisa has been taken hostage. Rejecting Nine's pleas to focus on their mission, Twelve sets off to rescue Lisa. (en)
- Nine hacks into the Metropolitan Police Department database searching for data. Twelve follows Lisa, concerned about her living on the streets. Nine sends a fourth video, titled "Time Shock Bomb," where he and Twelve present another riddle related to Oedipus Rex to find a hidden bomb timed to explode. Using the riddle, Shibazaki finds a website created by Nine and Twelve, which asks for a password related to three maxims inscribed at the temple at Delphi. Realizing that time is running out, the police raid an apartment building where Nine was recorded dropping off a suspicious package while Shibazaki is still trying to solve the riddle. Police officers breach the apartment, only to find a laptop instead of the expected explosives. Although Shibazaki solves the riddle a few minutes before the deadline, the timer doesn't stop as, as Nine puts it, the police are cheating. Afterward, all police files of the attacks are leaked online. At the same time, Twelve rescues Lisa from two police officers and takes her to their apartment. Nine is adamant that Lisa can't stay as they can't trust her. However, as they argue, Lisa, hungry and exhausted, collapses. (en)
- Nine and Twelve decide to play Five's chess game. Arriving at the terminal, Shibazaki and the officers see messages being given to Nine and Twelve from Five on the terminal screens. Twelve gets Lisa to create a distraction by setting off flares, which trigger a fire alarm. Twelve then hacks into the camera system, enabling Nine to rush to find Five's location without being detected. He confronts Five and holds her at gunpoint, demanding to know why she is interfering in their plans. She responds that she wants to settle things with him and reveals that Lisa has been caught and is being held captive at the bomb's location. Airport police arrive and fire at Nine, forcing him to flee where he briefly passes Shibazaki. Nine finds Twelve, who receives a phone call from Lisa, who is aboard an airplane that has a bomb on board and is on autopilot heading towards a terminal filled with commuters. Nine contacts Shibazaki, convinces him that the latest bomb is not theirs, and instructs him to infiltrate the control tower and take control of the autopilot system. Nine and Twelve then rescue Lisa from the plane, while Shibazaki enters the control room and forces one of the operators to divert the plane away from the terminal at gunpoint. The plane explodes without injuring anyone, and Shibazaki spots a masked Nine, who signals him in thanks before leaving. Five, the person responsible for the bomb, manages to escape, but she has kept Lisa's school ID card. (en)
- Shibazaki transfers to the police agency heading the investigation, to the dissatisfaction of several other detectives. Meanwhile, as Nine constructs another bomb, he deduces from the presence of counter-nuclear terrorism special forces that police are aware of his and Twelve's theft of the plutonium from the Aomori nuclear facility. Shibazaki learns that one of the men who stole the plutonium worked at the nuclear facility for a short time, but his identity has since been erased. Shibazaki then laments to Kurahashi that, as a Hiroshima native, he hated summer due to the fears held by the older townspeople who experienced the town's atomic bombing during World War II. Nine and Twelve send a third video with another riddle related to Oedipus Rex. Meanwhile, Lisa, unable to keep on living with her mentally unstable and abusive mother, runs away from home. Shibazaki solves the riddle during a live stream organized by the police, during which he announces the location of the newest bomb. Watching the live stream, the news coverage, and their own surveillance cameras, Nine realizes the police have connected them to the stolen plutonium. Kurahashi reveals to other officers the reason behind Shibazaki's demotion: fifteen years ago, he tried to investigate a cover-up of a death orchestrated by powerful people, who demoted him to the archives since he didn't want to play by their rules. (en)
- The police chief announces to a meeting of his task force that a unit of the American Federal Bureau of Investigation will join the investigation, surprising the other officers. Nine has a nightmare involving Five, and he and Twelve conclude that Five is continuing a game of chess the three played years ago back at the institution. Lisa offers to help them, and Nine reluctantly agrees. Kurahashi tells Shibazaki about his meeting with the FBI agents, which included Five, who were described as researchers from an American organization called the Nuclear Emergency Support Team . Posing as Sphinx, Five sends a public text message containing a riddle that can only be decoded via Caesar cipher. The answer is a set of coordinates leading to the International Terminal of Haneda Airport. The police are told to stand by on orders from the superintendent general, but Shibazaki and some others ignore the order and head towards the terminal. Knowing that a trap is being set by Five, Nine takes Lisa to the terminal with Twelve to avoid detection. Twelve then realizes that Five is using the terminal building as a chessboard. (en)
- Following Nine's announcement of the atomic bomb, Tokyo's population begins to evacuate. Lisa encounters a severely injured Twelve who collapses. Shibazaki reminds Hamura that Sphinx has killed no one and receives confirmation from his daughter Haruka that the bomb could explode in the stratosphere without causing fatalities. However, an electromagnetic pulse from the explosion would black out the country and disable any planes in flight. All commercial flights are ordered to land, and fighter jets are dispatched to intercept the bomb, but it has risen too high. Twelve regains consciousness and tells Lisa that he and Nine were always alone. The atomic bomb detonates, and the city is then plunged into darkness. It is followed by an aurora illuminating the sky formed by the radiation from the blast. The following day, passing Tokyo's abandoned buildings and streets, Nine sets up makeshift grave markers for the Athena Project children at the Settlement. He is joined by Twelve and Lisa, and the three then spend an enjoyable day together. As night falls, they are approached by Shibazaki, who promises that Project Athena will be exposed. Minutes later, U.S. helicopters arrive, and Nine withdraws a detonator and threatens to explode another atomic bomb. Under orders from their superiors to keep the American government's involvement in the investigation a secret, the soldiers open fire and kill Twelve. Shibazaki shields Nine and promises that Sphinx will be remembered. Nine surrenders the detonator before abruptly dying from the same affliction that killed Five.
One year later, Project Athena is exposed, leaving the Japanese government under media scrutiny. Lisa encounters Shibazaki at the graves of Nine, Twelve, Five, and the other project children. Lisa reveals that Nine used to listen to Icelandic music and that "VON" was Icelandic for "hope." (en)
- The police investigation reveals that high temperature thermite-based bombs were used in the attack. The building collapse left 27 people with minor injuries but no fatalities despite the large-scale destruction. Lisa returns home shaken by the incident. Her paranoid mother is upset because Lisa didn't reply to her many calls and accuses her of wanting to leave like her husband. Meanwhile, Nine and Twelve start work on a cellphone bomb. They release a second video with a riddle from Oedipus Rex hinting at their next bombsite's location. After deducing what appears to be the site referred to in the riddle, police move to the suspected location, a DNA laboratory. Shibazaki calls the police chief, Kurahashi, with an alternative interpretation of the riddle, suggesting that the bomb will be at the Roppongi police district office. After the bomb explodes in the district office instead of the lab, Kurahashi asks Shibazaki to return to the detective division from his exile in the archives. Kurahashi also shares information about the theft of the Aomori plutonium with Shibazaki, including the fact that the letters "VON" were found at both locations. Lisa follows Twelve to the scene of the explosion, but he threatens to kill her if she makes a wrong move. (en)
- Nine turns himself in to the police but refuses to speak to anyone but Shibazaki. He demands a press conference at a specific location and time, or he will activate the atomic bomb prototype. Shibazaki visits Shunzo Mamiya, who confesses that he created the Athena Project to revitalize Japan's national morale following the nation's defeat at the end of World War II. Five is hospitalized due to her deteriorating health as a consequence of the Athena Project experiments. She learns of Nine's surrender and desperately drives off to reach him. Five's accomplices pursue the police convoy carrying Nine to the press conference through Shuto Expressway, only to find that the truck is a decoy. Enraged and desperate, Five pursues Nine herself. Twelve catches them on his motorbike and stops the truck carrying Nine, but Five causes him to crash. FBI agent Clarence attempts to stop her, but she kills him. Five confesses to Nine that she always wanted to beat him but never could. Knowing that she is dying, Five gives him a brief kiss before committing suicide by detonating the spilled gasoline from her car. The Japanese airwaves are then hijacked by a prerecorded message from Nine stating that the countdown for the atomic bomb's detonation has begun. Declaring that this is the final message from Sphinx, Nine unmasks himself and bids the people of Japan farewell. (en)
- Nine and Twelve place a bomb on a passenger train, and when they return to the apartment, they find that Lisa had tried to prepare a meal for them, which she burned. Twelve later comments to Nine that even if the food was inedible, it was better than the bland and forgettable food at the institution. Nine and Twelve post another video with a riddle, saying that an explosion will occur unless it is solved before the deadline at 8.00 PM. Using clues from the riddle, Shibazaki concludes that the newest bomb is onboard a train on the Shuto Shinjuku Line. He also realizes that there is a connection between the bombings: the locations are linked to people connected to a seminar run by the Rising Peace Academy, a secretive non-profit organization. Time passes, and not only are there no reports of the bomb being recovered, but cellphone reception fails throughout the area. Twelve goes to deactivate the bomb on the train car while Nine tries to locate it but is cyber-attacked by someone from their past. Nine manages to find the correct location of the train car with the bomb and rushes to the station to remove it manually, throwing a smoke bomb into the carriage to force commuters off the train. However, one woman remains, and as he enters the train to save her, the bomb explodes. As Nine drags the commuter out of the wreckage, he receives a text message saying, "I found you ^^." Shibazaki confronts Kurahashi about the bombing, but he has the same information as everyone: they all thought the bomb squads would remove and deactivate the explosives; hence, they stood down. During their quarrel, a young woman is sitting nearby, quite pleased with herself. (en)
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