In Batman: Arkham City, the Penguin runs the museum hideout. Oswald Cobblepot has converted Gotham's old natural-history museum into a heavily fortified base inside Arkham City, using it to display stolen weapons, captured enemies, and criminal trophies.
Batman enters the museum while searching for Mr. Freeze, whom the Penguin has kidnapped. The museum's exhibits become part of the level's setting, including dinosaur displays, frozen specimens, and the underground chamber where Solomon Grundy is imprisoned. Penguin's gang also uses the building as a weapons depot and stronghold.
The Penguin is one of Arkham City's major crime bosses, alongside the Joker and Two-Face. A common mix-up is confusing his museum with the Joker's steel mill hideout or Two-Face's courthouse. The Penguin's later Arkham Knight operations are based elsewhere, including the abandoned shopping mall used for his arms-dealing network.
The museum sequence also introduces a major connection to Mr. Freeze: Penguin steals Freeze's equipment and holds him captive before Batman defeats Penguin and frees the cryogenic scientist.