Samples taken from Desmond Miles’ body in the moments after his death have enabled Abstergo Industries to continue to explore his genetic memories using the Animus’ newfound cloud computing abilities. The unnamed player character is hired by Abstergo Entertainment, from their Montréal headquarters, to sift through the memories of Edward Kenway, an eighteenth-century pirate, the father of Haytham Kenway and the grandfather of Ratonhnhaké:ton. Ostensibly, this is to gather material for an Animus-powered interactive feature film, but in reality, Abstergo—the Templars of the present time—are searching for a First Civilization structure known as the Observatory, and are using the memories of Edward Kenway to find it.
As Kenway, the player must unravel a conspiracy between high-ranking Templars within the British and Spanish empires who, under the guise of cleaning up piracy in the Caribbean, have used their positions to locate the Sage—later identified as Bartholomew Roberts—who is the only man that can lead them to the Observatory, a First Civilization device which can monitor anyone anywhere in the world when provided a blood sample, which they intend to use to spy on and blackmail world leaders. Kenway becomes an unwitting player in their plot when he kills a rogue Assassin, Duncan Walpole. Seeing an opportunity for profit, Kenway takes Walpole’s place at a meeting of Templars in Havana, where he meets Woodes Rogers as well as Cuban Governor, and Templar Grandmaster, Laureano Torres. His recklessness endangers the entire Assassins’ Order, prompting him to pursue the Sage and the conspirators from the Yucatán Peninsula to Jamaica, eventually catching Roberts on the island of Príncipe off of the African coast.