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.
Meanwhile, a band of notorious pirates—including Edward "Blackbeard" Thatch, Benjamin Hornigold, and Charles Vane, among others—dream of a pirate utopia where man is free to live beyond the reach of kings and rulers. With Kenway's help, they seize control of Nassau and establish a pirate republic. However, poor governance, a lack of an economy and an outbreak of disease bring the pirate state perilously close to collapse, with the founders divided on the best way forward. Kenway attempts to resolve the dispute, but is too late to stop the Templars from exploiting the situation for their own ends.
Eventually, Kenway and Roberts uncover the location of the Observatory and retrieve the artifact powering it, but Kenway is betrayed by Roberts at the last moment. After a brief stint in prison for the crimes of piracy, Edward escapes with the aid of Ah Tabai, the Assassin Mentor, and elects to join their Order. Chasing down Roberts and the Templar conspirators, Kenway retrieves the artifact and returns it to the Observatory, sealing it away for good. He is left facing an uncertain future with his newfound convictions until he receives a letter informing him of the passing of his wife and the imminent arrival of his hitherto unknown daughter, Jennifer Scott. Kenway travels back to England, promising Ah Tabai that he will one day return to continue the fight against the Templars. Some years later, Kenway, Jennifer (using her mother's surname in her memory) and Kenway's young son Haytham are about to watch a play in an English theatre.
In the present day, the player is contacted by John, Abstergo Entertainment's information technology manager. John convinces the player that their employers know more than they are telling, and encourages them to investigate in more detail. He convinces the player to hack several Animus terminals and security cameras, and then has them deliver the information taken to Shaun Hastings and Rebecca Crane, who are working undercover to infiltrate Abstergo. When the facility is locked down after the hackings are discovered, John arranges for the player to access the Animus' core, at which point Juno materializes into an incorporeal form. She reveals that although it was necessary to open her temple to avert disaster, the world was not ready for her, and she is unable to affect it or possess the player character as her agents intended. John is unmasked as the reincarnated form of the Sage and attempts to murder the player to cover up the failed attempt at resurrecting Juno, but is killed by Abstergo's security before he can do so, thus implicating him as the one responsible for the hacks. As Roberts, the Sage admits to Kenway that he owes no allegiance to the Assassins or the Templars and instead uses whoever he thinks represents his best chance of achieving his ends. With the Sage dead, the player is contacted by the Assassins as they continue their infiltration of Abstergo, but neither side is able to explain the Sage's presence or identify his followers, the Instruments of the First Will.[note 2]