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.
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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