It is located at the very southwest of Arkham City in the Bowery and was one of the biggest spots in the Prison. It held many crude exhibits, mostly being dead members of enemy factions like a dead Joker Henchman, a TYGER Guard, a Two-Face Henchman, and even had a League of Assassins Ninja.
Arkham Origins Incident
The Museum was seen on Christmas Eve, but since it was still operational at that point, it wasn't accessible because it was closed for the night. The Museum was also where Deathstroke was confronted by Black Mask's Henchmen as a test of his skill.
Arkham City Incident
When a chunk of Gotham was isolated and had all the inmates from Arkham Asylum were thrown into it, a three-way turf war broke out between Two-Face, the Joker, and the Penguin, all having a main base for themselves and their minions to settle in. When the Joker got deathly ill, he knocked out Batman, poisoned him and most of Gotham, and told him that only Mr. Freeze could make the cure.
Batman found the coldest place in Arkham City, the old GCPD Building, only to find that the Penguin had Mr. Freeze held prisoner at the Museum. Batman hacked his way in and fought his way through the Trophy Room, the Gladiator Pit, the Torture Chamber, the Museum War Room, and the Armory. Batman then went to the Iceberg Lounge, disabled Mr. Freeze's Freeze Gun, and Penguin had him fight Solomon Grundy, who lived under the Iceberg Lounge. In the end, Batman killed Grundy, defeated Penguin, and locked him up in the exhibit case that was meant for Bruce Wayne in the Trophy Room. Later, Two-Face overthrew the Museum and took Catwoman's loot, but only took half of it for himself, and gave the other half of it away to his henchmen and was knocked out by Catwoman herself.
- Two-Face: Contained 2 dead Two-Face thugs, one 'riding' a velociraptor fossil and the other scrunched up against the side. The ground is covered in grass and there's several 'Vote for Dent' posters. Recording: "Don't send your boys over here Harvey. Next time, I'll cut 'em in two. Come to think of it, you'd probably like that, wouldn't you?"
- League of Assassins: Contained a female League of Assassins Ninja (who was the same one who later broke out and accident lead Batman to Ra's Al Ghul) who was meditating in a room with lit candles and a background that resembles an ancient Chinese bedroom. Recording: "Now this little minx is a real puzzle. Where did she come from? How did she kill eight of my men before we managed to hold her down and beat her into unconsciousness? All I know is... I like her pajamas."
- Bruce Wayne: It showed a bag of money in a Bruce Wayne case. Recording: "A little bird told me that Bruce Wayne is on his way to be a part of my collection. When I get my hands on that spoiled little rich kid, I’ll make him regret what his family did to mine."
- Joker Henchmen: Contained 2 dead Joker Thugs on a roller coaster cart. Recording: "The joke is definitely on these losers! Tell me, what do I need to do to stop you sending these goons into my home, Joker? Kill you?"
- TYGER: Contained a dead TYGER Guard in a case. Recording: "Hugo Strange is watching you! Yeah, right. Pity he wasn't watching this TYGER Guard when we went to work on him with blow torches and iron bars."
- Victor Zsasz: It showed a broken case where Zsasz was imprisoned and escaped. Recording: "Take a good look into the eyes of a monster! A deeply disturbed serial killer, a man responsible for the murder and subsequent mutilation of over one hundred men, women and children. You are looking at... Zsasz!."
- Scarface: When you pressed the button he danced by strings. Recording: "Press the button and watch the puppet dance."
- Batman: It showed in Batman case some bats and a moon. Recording: "This will be the jewel in my collection! Coming soon!... the Batman!"
- Mr. Freeze: Mr. Freeze was imprisoned in a display case. Recording: "Surely no introduction is necessary. A prize- winning cryogenic scientist pushed to the edge of sanity by a desire to help his poor, dying wife... or an old man, captured by me and stuck on the grill?"
- Harley Quinn: It showed one of the Harley Heads in a case. Recording: "This one just waiting for the clown's girlfriend to show up, she'll be good for a few minutes of entertainment before I... cut her head off."
- The Joker: It showed a Joker mannequin in a case with a TV head. Recording: "The Clown Prince of Crime. Bah! This guy needs putting down like a sick puppy. He's been inconvenience to my operations too long and to be honest, I really don't find him that funny."
- Bud and Lou: Contained Joker's two stuffed deceased hyenas. Recording: "Recognize Joker's pets? Me too. That's why I had them shot and stuffed!"
- You could find a Batarang on a magazine with Joker's face in the War Room.
- Tiny didn't attack and kill you after you defeated Penguin.
- One of Penguin's Henchmen said that there were spots for Catwoman and Robin in Penguin's collection, but the one for her never showed up.
- The DLC Challenge Map in Arkham Origins "Venom Connection" was designed like the Museum.