Shay Patrick Cormac (Steven Piovesan) is a new recruit to the Colonial Brotherhood of Assassins whose potential is offset by his insubordination. While training with the North Atlantic chapter under the Assassin Mentor Achilles Davenport (Roger Aaron Brown), he encounters the Assassin Adéwalé (Tristan D. Lalla), who brings news that the Haitian city of Port-au-Prince has been devastated by an earthquake during the search for a Precursor temple containing a Piece of Eden. With his experience captaining ships—including the recently acquired Morrigan—Cormac is enlisted in an investigation into Templar interests in a Precursor artifact and manuscript that are linked to the temple.
Posing as a Templar courier, he delivers the artifact and manuscript to Benjamin Franklin (Rick Jones) whose experiments with electricity on the artifact generate a map showing the location of Precursor temples around the world. He identifies one in Lisbon, and Cormac is dispatched by Davenport to retrieve the Piece of Eden it contains. However, Cormac has begun questioning the Assassins’ motives after seeing their refusal to engage in dialogue with the Templars, and being asked to kill an already-dying Templar commander, Lawrence Washington. His convictions are destroyed in Lisbon when his efforts to retrieve the Piece of Eden trigger a massive earthquake, destroying the city. Correctly deducing that a similar sequence of events destroyed Port-au-Prince, Cormac is horrified to learn that Davenport intends to continue the search for Pieces of Eden despite the danger. Shay then steals the manuscript and attempts to escape the Homestead, but is cornered by members of the Brotherhood. Intending to commit suicide by jumping off the Homestead’s cliff, Shay is shot and left for dead before he can destroy the Manuscript.
Now that he is cast adrift, he finds himself in New York City, acting as a vigilante to clean out gangs that are extorting the citizenry. His efforts attract the attention of Colonel George Monro (Graham J. Cuthbertson), who convinces Cormac that he can improve the lives of others. Meeting with Christopher Gist, Shay retakes his ship the Morrigan from the Assassins, and agrees to assist his new allies, despite learning that they are Templars. He is disturbed to learn that the Assassins have not given up their search for the Pieces of Eden, and believing them to be a threat, commits himself to the Templar Order to hunt them down. After killing Colonial Brotherhood Assassins Le Chasseur (Chimwemwe Miller) and Kesegowaase (Danny Blanco-Hall), Shay becomes a fully fledged member of the Order when he is inducted by Grand Master Haytham Kenway (Adrian Hough). Shay then eliminates Adéwalé, Hope Jensen (Patricia Summersett) and Louis-Joseph Gaultier de La Vérendrye (Marcel Jeannin). Finally, only two senior members of the Assassins in America remain alive: Achilles himself, and his second-in-command Liam O’Brien (Julian Casey), once Shay’s best friend. Shay pursues the two to the Arctic with Haytham, where the Assassins have located another Temple. Having dispatched most of the Assassin expedition, Shay and Haytham enter the Temple to find Liam and Achilles, who have realized that the artifact is as Shay said—a means to stabilize the world, not a weapon to control it. However, Achilles’ attempt to stop Liam taking vengeance causes the artifact to be destroyed, and a third earthquake is triggered. As the four try to escape, Shay and Liam duel on the ice and Liam is fatally injured when the two fall. Shay then makes his way back to his ship and arrives as Haytham overpowers Achilles. Shay persuades Haytham to spare Achilles, out of mercy and to ensure knowledge of the Temples will not be lost, so the Assassins will not try to pursue them again. Haytham then shoots and cripples the last American Assassin, who retires to his homestead near Rockport, Massachusetts (paving the way for the events of Assassin’s Creed III).
As the Templars set sail for home, Haytham tasks Shay with retrieving the Precursor artifact. Shay spends the next 16 years hunting it down, even as Templar influence in the colonies was eventually destroyed by Connor during the American Revolution. The final memories gradually reveal a mission to escort Benjamin Franklin through Paris, in search of the Precursor box that is in the possession of Charles Dorian, a French Assassin and the father of Arno Dorian (the protagonist of Assassin’s Creed Unity). Shay murders Dorian and takes possession of the box as he becomes a senior member of the Templar Order.
In the present day, the player is researching Cormac’s memories for Abstergo Entertainment when they inadvertently trip a hidden memory file that infects the Animus servers. Abstergo is placed in lockdown, and the player must clean the Animus servers out by living Cormac’s later memories. Juhani Otso Berg, a senior member of the Templars, later orders the player to upload Shay’s memories to the Assassin servers in order to weaken their resolve by showing how close Achilles Davenport came to destroying the world and the Assassins betraying Shay. The Brotherhood responds by cutting off their communications. In a mid-credits scene, Berg thanks the player for their help, and gives them a choice: join the Templar order, or die. The scene fades to black before the player’s decision is shown.