Someone is killing androids in Paradigm City. After several attacks, Paradigm HQ dispatches a special agent to assist in the case: Freddy O'Reilly. But Freddy is an android himself. He and Dastun have an uneasy working relationship. When Dorothy is targeted, she manages to avoid being destroyed and is taken in for police questioning.
Roger is still having strange flashbacks. He can only assume that they are memories, but he's not quite sure. Frustrated, he returns to visit Gordon Rosewater, the man who built Paradigm City, on his farm. Gordon only offers vague platitudes and cryptic responses, until he gives Roger one very important clue.
Dorothy is in danger, and thanks to Dastun's police cruiser, Roger manages to rescue her from Alan Gabriel's clutches. Alex Rosewater arrives in his newly-resurrected Big Fau and destroys the Megadeus that damaged the Paradigm City dome. However, once the enemy is defeated, Alex is unable to control the Big Fau, and it continues firing wildly.
Roger is unsympathetic to Alex's problems. Alex pushes his science group to reactivate the Big Fau. Underground tremors and a power outage draw attention to these tests, and the union spy Vera unleashes a three-headed giant electric eel. Once again, Roger and the Big O find themselves facing a giant monster to protect all of Paradigm City.
Roger's mansion is under attack by Beck and his droid forces, all arranged by Paradigm Corporation and Alan. They are not after Roger Smith, but the one who possesses the memories that can resurrect the Big Fau: Dorothy. Even though Dorothy did not realize the existence of these memories, she is still pursued relentlessly.
In the Big Fau and Big O battle, Big Fau's immense and superior powers push Big O to the limit. Dorothy, sensing that Roger is in danger, suddenly becomes conscious from her deep sleep and saves Roger from defeat. Angel and Gordon enter into another dimension to return to a life with certainty...that is, a life without missing memories.
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