Following the destruction of Miguel Soldano's wayward creation Dorothy-1, Paradigm City's residents contend with the aftermath. R. Dorothy Wayneright suddenly disappears, seemingly distraught by the sight of watching her sister creation be destroyed. Angry that the surrounding cityscape was collaterally damaged by Big O, Dan Dastun commands the military police to open fire on it as it returns to its underground base. Back in his car, Roger divulges that an extensive underground rail system exists as a relic of the city's bygone past. Unaware of its original intended purpose, he now uses it to transport Big O around the city.
Roger returns to his contact and wonders how a Megadeus like Dorothy-1 could have been refurbished, to which his contact reveals that Dorothoy-1 was newly built: seemingly an impossibe feat for someone in an amnesiac city with no supposed technical memory of constructing robots. At night, Dorothy is seen with Timothy Wayneright I, introduced as her grandfather at a nightclub. Roger deduces that Wayneright was Dorothy's true "father"; she was contructed by Miguel Soldano using Timothy Wayneright's memories as blueprints. Jason Beck appears at the nightclub and shoots Wayneright after having taken him hostage and captures Dorothy after she tries to escape. Post-mortem investigation reveals that Timothy Wayneright was a scientist who managed to regain his memories for designing Megadeus robots. Wayneright's actual daughter, after whom Dorothy was modeled, died in the accident that happened 40 years ago.
A critically damaged Dorothy-1, with Beck revealed to have been its pilot all along, returns and runs amok in Paradigm City once again. When Roger tries to finish off Beck, he sees Dorothy wired into Dorothy-1, being used as a power regulator circuit. Roger, hesitant to fight back, climbs out of Big O and pulls Dorothy out, making Dorothy-1 useless and trapping Beck for his arrest. Beck would come to admit that Wayneright had been a client of his; desperate to resurect his late daughter any way he could, he used the blueprints of Dorothy-1 to raise the money to do so. Roger opines that Wayneright found closure after spending the evening with Dorothy at the nightclub. Following the aftermath of Wayneright's death, Dorothy decides to reside with Roger as his maid.