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The biggest obstacle when designing the game was integrating the Batmobile. During early development, Rocksteady placed a prototype Batmobile in the existing Arkham City map, and learned that the claustrophobic city designed for Batman to glide and grapple did not work well for driving a vehicle. Gotham City was thus redesigned to accommodate the new mechanics.

The designs for the Batmobile were based on the earlier design from Arkham Asylum, instead of models from the history of Batman comics and media, and evolve that to meet the necessary gameplay requirements.
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Spoiler:During the final hallucination of the game where the player is controlling a gun-wielding Joker, as he guns down Penguin, Riddler and Two-Face, the song "Only You (And You Alone)" by The Platters can be heard playing on a radio throughout the corridor where the villain trio are cowering.

This was the same song that Joker himself sung in the end credits of Batman: Arkham City.
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The scene in whichSpoiler:Batman must escape an exploding Ace Chemicals seems to be a nod to a scene from Tim Burton's 1989 Batman film Spoiler:where Batman rides through an exploding chemical plant.
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When the game first released on Steam, Arkham Knight was horribly optimized and panned by customers and media alike. The game was taken down and eventually replaced months later.

However, one running joke was that the original buggy game ran at the speed depicted on a speed limit sign in the game's promotional art, which was 30 miles per hour (or 30 fps on most systems). This artwork was changed when the game was re-released on Steam, now showing a 60 miles per hour speed limit and serving as a subtle nod to the game's performance fixes.
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Attachment Spoiler:In the DLC "Matter of Family", a hidden room can be found between the Ferris Wheel and the Great White. Inside the room the player can find DC villian Starro the Conqueror in a containment tube.

In front of the Great White is a billboard with another reference to this villain and its "mind control" ability.
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A Mac and Linux port were planned to be released and was being worked on by Feral Interactive, with a Spring 2016 release. However, it was later announced on Steam that it had been canceled with refunds offered to anyone who had pre-ordered a copy.
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Spoiler:During the scene in which Batman is forced to watch Oracle kill herself, The Joker can be seen nudging the gun she uses closer to her, which should be impossible as The Joker is only a hallucination in Batman's mind. This is actually a subtle foreshadowing to later in the game where it is revealed the entire scene was a hallucination.
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Before the boss fight against the Arkham Knight in his tunnel excavator, the Arkham Knight says that he asked if the excavator came in black, a nod to the line from the Christopher Nolan film Batman Begins.

The Arkham Knight also remarks how Batman always "gets knocked down only to pick himself up again." This is another nod to a line spoken in the film. Spoiler:Additionally, the Knight says he learned this from an "old friend". Because Alfred is the one who spoke the line in the film, this is also a hint at the Arkham Knight's true identity.
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In the A Matter of Family DLC, the Joker will sometimes call Batgirl "Bat-fake", a reference to the insult he called Terry McGinnis in the animated movie Batman Beyond: Return of the Joker.
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Sefton Hill stated on reddit that they were originally going to include an interactive combat battle against Rocksteady employees, in the game's credit. And each time the player got a knockdown, the developer's names and roles in development to appear during the slow-motion. It would've been used for the new game plus, but due to time constraints, they have to remove this feature.
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If the player detonates explosive gel inside Penguin's vault, the stack of bombs turns into an unused destroyed Titan canister model that appears to have been carried over from Batman: Arkham City, although it is impossible to go back inside the vault to interact with it.
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