As a homage to the former book, the game's subtitles rendered each noun with capital letters, while Woodard was invited to consult on the game. McDevitt stated the game's primary history resources were Captain Charles Johnson's A General History of the Pyrates (1724) and Colin Woodard's The Republic of Pirates (2008).

He considered beginning the story with Edward as a boy during William Kidd and Henry Morgan's era of piracy, but decided he felt skeptical as to whether Assassin's Creed II convincingly portrayed a similar span of time, and so opted to simply focus on the Blackbeard era towards the end of the Golden Age of Piracy.

Writer Darby McDevitt began writing the game soon after completing Assassin's Creed: Revelations, after being suggested to do a game expanding the 'Kenway family saga', instead of Connor's life story as they did with Ezio Auditore. Ubisoft's Montreal-based team, in conjunction with 7 other studios from Singapore, Sofia, Annecy, Kiev, Quebec City, Bucharest and Montpellier-accompanied by a band of developers of Far Cry 3-contributed to the completion of the game, with each studio focusing on different elements. The pair also explained that because the game was so radically different from its predecessor and that the scope and open-world gameplay was so different from the previous game, they opted for the project to be a numbered sequel as opposed to a spin-off that followed in the footsteps of the last numbered game, Assassin's Creed III. Ismail also stressed that they aimed towards a more historically accurate take on the era, including staying away from the stereotypical image associated with pirates, such as parrots, Krakens, and plank-walking. Assassin's Creed IV: Black Flag producer Martin Schelling and Mission Director Ashraf Ismail both stated that they began the project in the summer of 2011, with a pirate game as their focus.

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