After Sequences 3-5

In this chapterBartholomew Roberts, later identified as the Sage, holds the key to locating the Observatory, a device that can monitor anyone in the world when given a blood sample.

The Observatory is a First Civilization device that can watch anyone with a blood sample. Roberts, who turns out to be the Sage, leads Edward to it, and then betrays him. Edward is arrested at Port Royal as the Republic falls apart. The Observatory introduces the franchise's surveillance theme. Whoever controls it can find anyone.

Roberts' betrayal shows that even the pirates have their own ambitions.

In this chapterAh Tabai, the Assassin Mentor, orchestrates a prison rescue, freeing Edward along with Anne Bonny and Mary Read.

Ah Tabai frees Edward from prison and Edward joins the Assassins. He eliminates the main Templars, including Woodes Rogers, Roberts and Torres, and seals the Observatory. He learns that Caroline has died and that he has a daughter, Jennifer. In London he goes to the Opera with Jennifer and his son Haytham.

Edward's change from a selfish privateer to a man who cares for his family is the game's main arc. The final scene at the Royal Opera House connects with Assassin's Creed III, where Haytham is later seen at the same theatre.

In this chapterThe employee discovers that John Standish, the facility's IT manager, is a Sage attempting to resurrect Juno.

In the present, the player is an Abstergo Entertainment employee in Montreal who is making a game from Edward's memories. During this work, the employee finds out that the IT manager, John Standish, is a Sage trying to bring Juno back. The modern frame is a satire of corporate entertainment, and it keeps the franchise's modern conflict alive after Desmond's death.

Standish's reveal ties the Sage storyline from Edward's time to the present.