Naval aspects from previous games return with the player controlling Shay's ship, Morrígan. Morrígan has a shallower draft compared to Edward Kenway's Jackdaw from Assassin's Creed IV: Black Flag, allowing for river travel. New features include new ship-based weapons such as releasing an oil slick which can then be ignited, Puckle guns, and the ability for enemies to board Morrígan during ship-to-ship combat. The arctic environment also features into naval gameplay and exploration, as certain icebergs can be rammed with an icebreaker.The underwater diving missions featured in Black Flag do not exist in the North Atlantic, as swimming causes the player's health to rapidly deplete due to the frigid water.
For combat, the game introduces an air rifle, which allows the player to silently take out enemies at a distance. The air rifle can be outfitted with a variety of different projectiles, such as firecrackers. The player can also use a grenade launcher, which fires off shrapnel grenades and other loads.Hand-to-hand combat has been slightly altered, and now enemy attacks can be countered with timing, similar to the Batman: Arkham series of games. Enemy Assassins feature archetypes similar to previous games, using skills that players have been using throughout the series; they can hide in bushes, blend in with crowds, and perform air attacks against the player.Poison gas can now be used as an environmental weapon, and Shay has a mask that can mitigate its effects.
Side missions and activities return, with a number of them based on those of the previous games. Reflecting Shay's role as a Templar, the game introduces a new side mission: Assassin Interception. These mirror the Assassination side missions in previous games, in that Shay, after intercepting a messenger pigeon carrying an assassination contract, must prevent a Templar agent being assassinated by finding and killing Assassins hidden nearby.
The main character of the game is Shay Patrick Cormac, a twenty-one-year-old recruit to the Brotherhood of Assassins who grows disillusioned with their methods and their cause just as his career as an Assassin begins.He eventually betrays and abandons the Assassins after an assignment ends in disaster, and is later accepted into the Templar Order, offering his services as an Assassin Hunter after seeing some of the Assassins groups used as allies have taken to terrorizing New York. Given access to near-limitless resources, Cormac sets out against his former companions, with his actions having dire consequences for the future of the Brotherhood.Cormac has ties to the events that occur in Assassin's Creed Unity.Appearances from previous Assassin's Creed characters include: Haytham Kenway, the secondary antagonist of Assassin's Creed III;Achilles Davenport, Ratonhnhaké:ton's mentor; and Adéwalé, Edward Kenway's quartermaster in Black Flag, and protagonist of Freedom Cry.
The Modern Day plot begins one year after the events of Black Flag, with a new unnamed player character that works for Abstergo Entertainment. While investigating the memories of Shay Patrick Cormac, an Assassin working in the North Atlantic during the French and Indian War, they inadvertently trip a hidden memory file that corrupts the Abstergo servers. With the building being put into lockdown, the player is recruited by Melanie Lemay to continue exploring Cormac's memories in an effort to clear the system.
Cormac is a new recruit to the Brotherhood of Assassins, working under Achilles Davenport. Achilles sees potential in him, but Cormac develops an insubordinate streak that frustrates his mentors. Believing that taking a more active role in the Brotherhood's affairs will temper his impetuousness, Achilles orders Cormac with his newly acquired ship the Morrígan to track down a Templar cell that has been deciphering a Precursor artifact revealing the locations of several Pieces of Eden. The artifact, in the form of a wooden box, had been stolen from the Assassins following a massive earthquake in Haiti some years before. With the help of Benjamin Franklin, a Piece of Eden is located in Lisbon, and Cormac is tasked with retrieving it.
However, Cormac has begun questioning the Assassins' motives after seeing their refusal to engage in dialogue with the Templars, and takes no satisfaction from killing an already-dying Templar commander, Lawrence Washington. His doubts come to a head in Lisbon, where his attempt to retrieve the Piece of Eden triggers an earthquake that destroys the city. Noting that similar events occurred in Haiti, Cormac is horrified to learn that Achilles and the Assassins intend to pursue the remaining Pieces of Eden. Cormac steals a manuscript necessary to interpret the artifact and flees, while the Assassins give chase. Confronted at the edge of a cliff in the homestead, he decides to commit suicide and bury the manuscript to the depths of the Atlantic than to let the Assassins reacquire it. Just as he jumps, an Assassin shoots him in the back; Cormac comes to believe it was his best friend Liam's doing.
Cormac is rescued by a passing ship and taken to New York City. Once he recovers, he uses the skills he learned from the Assassins to drive out the city's criminal gangs. His actions attract the attention of George Monro, the city's governor, who offers Cormac the chance to help rebuild the city. Indebted to Monro, Cormac assists the British Army in their early campaigns against the French, and discovers that Achilles' chapter is supporting the French war effort. Monro reveals himself to be a Templar, and despite knowing of Cormac's prior loyalty, offers him a place within their Order. Cormac accepts, but Monro is killed shortly afterwards during an attack on a British fort. Cormac is then formally inducted by the Templar Grandmaster, Haytham Kenway.
Cormac reveals to Kenway his belief that the Pieces of Eden sought by the Assassins are not weapons, but are instead being used to hold the world together, and he pledges to stop his former allies before they cause another catastrophe. His efforts lead to the deaths of several senior figures in the Brotherhood, until only Achilles and Liam remain. Having discovering that the pair are headed for another Precursor temple in the Arctic, he immediately pursues them. Inside the temple, Haytham and Cormac confront Achilles and Liam over their actions, but Achilles' attempts to prevent bloodshed causes Liam to destroy the Piece of Eden by accident, causing another earthquake. While Haytham pursues Achilles, and Cormac and Liam fight throughout the temple, until Cormac ultimately kills his former friend. He arrives in time to persuade Haytham to spare Achilles, as his testimony will stop the Assassins from trying to locate other temples. Haytham nonetheless cripples Achilles as a precaution by shooting him in the knee.
With the Assassin Brotherhood all but destroyed, Cormac is tasked with locating the artifact that was used to find the Pieces of Eden, as Achilles had passed to other Assassins prior to his Arctic voyage. Cormac's twenty year search eventually leads him to Versailles, where he discovers it under the care of Charles Dorian; father of Arno, protagonist of Assassin's Creed Unity. Cormac kills Charles and takes possession of the artifact, taunting the dying man with the promise that while the American Revolution ended Templar influence in the Americas, a new revolution may yet hold promise.
In the present day, the player reconciles Cormac's memories. Under the direction of Otso Berg, a senior Templar leader, they upload them to the Assassin network, revealing how close Achilles Davenport came to destroying the world. The result is almost instantaneous, with the Assassins thrown into disarray and, as revealed in Assassin's Creed Unity, retaliating by hacking into the Abstergo's systems and destroying all of the company's Precursor samples as well as causing several of their servers to melt down. As reward for their actions, the player is presented with a choice; join the Templar Order, or die. The game fades to black before a choice is made.