The battle is over. Dazed and confused, Roger wanders the streets, but this is not the world he remembers. Here, the Big O is nothing but a comic book fantasy. His home is actually a bank, and he is a homeless wanderer. Are his memories merely the delusions of a man gone mad?
Fully recovered, Roger is hired to protect one of Paradigm City's Senators, Roscoe Fitzgerald, from an assassination attempt. The clues lead back to Dorothy's creator, Doctor Wayneright. However, when they investigate his home, they set a terrible plan in motion and the Megadeus Glinda is unleashed on Paradigm City.
Something crashes to Earth outside the domes of Paradigm City. The locals think it's an angel, a messenger from the heavens, but a Paradigm Corporation investigation team removes it. When Roger investigates, he runs afoul of Alex Rosewater again. Since Alex doesn't care about objects from the sky, it's up to Roger to save countless lives.
Schwarzwald is still alive, and he is distributing leaflets about the arrival of a great Leviathan. Needless to say, Alex Rosewater wants him stopped, and Paradigm Corporation tries to hold Roger to his old contract. Later, Paradigm City is indeed attacked by a Leviathan, but instead of mythical beast, it looks like another Megadeus.
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.
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