The Wayne Manor is rumored to be haunted so Gordon and his troop of Gotham Police go to investigate.
Two children run out of the abandoned Wayne Manor, screaming in fright and claiming that the house is haunted. One of them runs into a police officer and tells his wild tale. The news circles back to Commissioner Gordon who goes to the Wayne Foundation to ask Bruce Wayne for permission to inspect the house. Bruce doesn't want the GCPD accidentally stumbling upon the old Batcave, so he politely denies Gordon's request. Gordon snaps and angrily tells him that he is going through with the investigation whether Wayne likes it or not.
Meanwhile, Rupert Thorne returns to Gotham City after being locked away in Arkham Asylum for a over a year. He re-establishes his position at the Tobacconists' Club and tells his fellow members how he intends on putting his own political stooge in the mayor's office. He blackmails the other club members into supporting his scheme.
Commissioner Gordon hires famed ghost breaker Doctor Terrence Thirteen to accompany his officers on an inspection of the manor. Also in attendance is Miss Crum, manager of the Gotham Historical Society who has been administering to the upkeep of the mansion ever since Wayne abandoned it.
Batman secretly arrives at Wayne Manor and tries to seal off all of the known entrances to the Batcave. He detects that someone else has been inhabiting in the Batcave and begins exploring. Suddenly, the Man-Bat swoops down out of nowhere and attacks him. Doctor Thirteen enters the Batcave just as the Man-Bat grasps Batman by the throat.