Sea shanties return, with a mix of old and new ones. Puckle guns are introduced, ships can be rammed, and the Morrigan can be boarded by enemies during ship-to-ship combat. There are also new weapons such as oil barrels that can be ignited. His ship Morrigan is smaller and can be used to travel through rivers. Swimming in icy water damages Cormac's health and there are no underwater missions like in Black Flag. The ice in the latter environment introduces new game mechanics, such as frozen cargo, icebergs used as cover and an ice-breaker ram to open up passages.

The game's main locations are New York, the River Valley and the North Atlantic Ocean. The game is set in the 18th century during the French and Indian War. The familiar modern day sequences also return, this time playing as a new employee at Abstergo Entertainment who needs to explore Cormac's memories during a server crash. Many characters from the aforementioned games return, including Adewale from Freedom Cry. He eventually becomes disgruntled with the order's tactics and becomes involved with the Templars as a feared Assassin Hunter, making it the first title in the series to control a Templar throughout the larger portion of the game. The protagonist is Shay Patrick Cormac, an Assassin recruit with a rebellious streak. Most of the gameplay and design is similar to the sandbox environment of Black Flag as the game combines exploration on land with ship-based naval exploration and battles. It also acts as a prequel to Assassin's Creed III and the game's final mission is a prologue to Assassin's Creed: Unity, which was released simultaneously. It is the sequel to Assassin's Creed IV: Black Flag from the year before. Assassin's Creed: Rogue is the eighth main game in the historical series.

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