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's entertainment division to sift through the memories of Edward Kenway, an eighteenth-century pirate and the grandfather of Connor. Ostensibly, this is to gather material for an Animus-powered interactive feature film, but in reality, Abstergo and the Templars are searching for the Observatory, a Precursor structure that allows the user to see through the eyes of a subject. As Kenway, the player must unravel a conspiracy between high-ranking Templars to manipulate the British, Spanish and French empires into locating the Sage - later identified as Bartholomew Roberts - who is the only man who can lead them to the Observatory.
In the present day, the player is contacted by John, Abstergo Entertainment's information technology manager. John convinces the player that his employer knows more than they are telling, and encourages them to investigate in more detail. He arranges for the player to access the Animus' core, at which point Juno materialises 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. 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.