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In an interview with Kotaku, Sefton Hill, game director at Rocksteady Studios, revealed that there was going to be a scene referencing the shark repellent from the 1966 film "Batman: The Movie" starring Adam West. At the part when Tiny the shark bites into Batman's raft, Batman would reach for a compartment on his Utility Belt labeled "shark repellent". Opening the compartment, Batman would pull out brass knuckles which he then uses to beat Tiny with.

"One of the ideas we originally had is the shark comes out and grabs the raft. And then Batman pulls out shark repellent and he opens it up, and inside the shark repellent was a massive knuckle duster. And he just smashes the shark on the nose. And then we thought: maybe the tone is going a bit wrong… then we thought we'd slip it in for New Game Plus. We decided not to."

However, a remnant of this idea is still on the final game. If the player loses against Tiny, one of the Game Over screens leaves the following hint: "Fight off the shark using Batman's powerful shark repellent: a flurry of furious strikes."
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The game's first teaser trailer featured Harley Quinn in her costume from Batman: Arkham Asylum, though a completely new costume is seen in the final game. It is possible this trailer was made before a different costume was considered.
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The Catwoman Episodes initially ended with her coming to Batman's aide, but late in development, the developers decided to give the player an alternate choice, allowing them to have the morally-grey Catwoman leave the city with her loot; the addition was implemented in two days.
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The developers had considered adding a multiplayer element to the game, but ultimately decided against it.

According to Hill: "If we use all of the energy that is required to create multiplayer and instead focus this on the single player, would that deliver a better overall game?", and decided in the affirmative.

Multiplayer would later be a feature in Batman: Arkham Origins
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Although the Robin seen in this game and Batman: Arkham Knight is Tim Drake, his "Animated Series" skin is of Dick Grayson as Robin.

Dick Grayson as Nightwing appears as a challenge mode-only DLC character.
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Wearing Batman's "Animated Series" skin during the main story will result in Catwoman and Robin appearing in their respective Animated series skins as well. This also works for the "Harley Quinn's Revenge" DLC should the player exit out of it, continue from the main menu and select the Animated series outfit there.
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Kevin Conroy, the iconic voice of Batman, described the game as "really, really dark." While relating the game's dark nature to the animated movie Batman Beyond: Return of the Joker, Conroy also said, "It involves a lot of the villains and it goes to that area - it's that dark."
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The original idea was to take the game out of the asylum setting and onto the streets of Gotham City while retaining the level of design detail put into the asylum. Rather than a series of generic streets, the team wanted to include locations from the Batman mythos that were not only notable but meaningful to the character. Rocksteady was initially unsure how technical considerations would limit the scope of this idea.
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The Detective Vision was redeveloped for Arkham City because it was considered to be too useful in Arkham Asylum, resulting in some players using it throughout almost the entire game; the visual effect also obscured the game's design aesthetic. One idea was to introduce a time limit on its use, but it was considered that Batman wouldn't make a gadget like that. Instead, it was designed to be difficult to use in certain situations.

The idea for a time limit on the Detective Vision would later be used in Batman: Arkham Knight.
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The design team chose to have Batman start the game with access to the gadgets unlocked in Arkham Asylum, to convey the impression that Batman is fully prepared for the inevitability of things going wrong in Arkham City.
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Rocksteady decided to not include the Batmobile, because it would be unable to travel on the city's broken terrain. Instead the team focused heavily on gliding as a sufficient means of transportation, and it was considered that putting Batman in any vehicle would make it a completely different game.

By the time they had programmed Batman to dive and glide between buildings of the asylum, the adaption of the gameplay to the city was considered natural.
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Rocksteady decided early on that the Joker would die in the story, and developed the idea of him poisoning Batman with the same affliction, in order to show how the two diametrically opposed characters would interact in pursuit of a shared goal. Warner Bros. and writer Paul Dini did not oppose killing off the character as long as it was not done for shock value, and as long as they made it clear that Batman was not at fault, since he would not intentionally kill someone.
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Batman's sidekick Robin also appears, featuring a shaved head and contemporary costume design that were intended to move away from his traditional "Boy Wonder" image.

Senior concept artist Kan Muftic explained:

"Our vision of Robin is the one of a troubled young individual that is calm and introverted at times, but very dangerous and aggressive if provoked. The shaved head is inspired by cage fighters, because we thought that Robin might be doing that in his spare time to keep him on his toes. Still, we kept all the classic trademarks of Robin's appearance, such as the red and yellow colors of his outfit, the cape and the mask."
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In the Park Row district, in the alley around the back of Monarch Theater, the player can find a chalk outline in the shape of two dead bodies. This is the same place where Bruce Wayne's parents, Thomas and Martha Wayne, were killed by a mugger while the family were on their way home from the theater. This incident of course led Bruce to become Batman.

Around the outline, a bouquet of flowers and an interview tape from Hugo Strange can be found on one side, with said tape consisting of a single message from Strange taunting Bruce/Batman. On the other side of the outline is a single red rose. A button prompt triggers when near this rose allowing the player to pay their respects to the Waynes. Batman will kneel by the outline in silent contemplation.

Staying in this position for a minute will earn the player an achievement/trophy for paying respect to the Waynes.
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Setting the date of the console or PC that the game is running on back to December 13th, 2004 (the day the game's developer, Rocksteady, was founded) and talking to Calender Man in the court house basement triggers special dialogue from him where he claims that "the end is near" and when it comes, he'll be there. This is likely a reference to the final game of the series, Batman: Arkham Knight, which was in development at the time, as well as it being the final entry in the Arkham game series.

This easter egg wasn't found by fans until 3 years after the game's release, when Rocksteady hinted at it's existence.
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After the cutscene in which Spoiler:Wonder Tower explodes and Ra's stabs himself, his dead corpse can be seen hanging from the gate. After completing the story, his body will be gone and his sword will be left at the foot of the gate.
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After the boss fight with Spoiler:Ra's, the player can either exit and continue the story or head back the way they originally entered. Heading back will lead to a dead end with a locked gate. Using a remote controlled batarang on the button its connected to, Killer Croc, a villain featured in Batman: Arkham Asylum, will burst though the wall and talk to Batman. This is the only time Killer Croc appears in the main game.
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In the "Iceberg Lounge VIP Room" Challenge Map, Killer Croc can be seen sitting in the background smoking a cigar and having a drink. The Penguin can also be seen looking on.
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During Protocol 10, the guardians of Wonder City will be stacked in a pile in the middle of Wonder Avenue. After Protocol 10, all guardians will be gone.
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In "The Joker's Carnival" Challenge Map, reaching a 100 hit combo will cause the Joker to join the fight. He will have the same moves he has from the story mode and does not affect the score in the challenge.
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