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?
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.
Beck is back. After engineering yet another escape from prison, he hooks up with a Japanese engineering firm. He also kidnaps Roger and vows to make him pay for all the humiliation he's suffered. Dorothy then takes the case as the negotiator, much to Dastun's chagrin. Once rescued, it's Roger vs. Beck in another giant robot battle.
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'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.
Alan, as the Dominus of Big Duo, gets into an intense battle with Big O. But as the battle reaches its climax, the hidden powers of the Megadeus are overpowering. Schwarzwald, who appears as the ghost of the former Dominus of Big Duo, sends Alan a message. Meanwhile, Rosewater manages to steal Dorothy's memory and install it into the Big Fau.
The Big Fau is resurrected and Paradigm city is about to disappear underneath the rubble by its destructive powers. Gordon Rosewater tells Angel about the true facts of her life and she is shocked to hear about her true identity. Meanwhile, Big O and Big Fau are hungry for memories, facing off to decide the fate of Paradigm City.
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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