Assassin's Creed: Pirates is a nautical, pirate-themed game spun off for mobile devices from Assassin's Creed IV: Black Flag. Players control the slave Alonzo Batilla who was saved by the French pirate Olivier Levasseur (La Buse). He is given a small ship and now roams the Caribbean seas for treasure. Pirates borrows the nautical elements from Black Flag, but has no ties to the story of Templars and Assassins, even though he will meet some from both factions occasionally, nor does it contain the exploration on foot from Black Flag.

All the gameplay takes place on the ship. It is viewed from a first-person perspective with a third-person when going at full speed. Swipes are used to look around the ship and by tapping, holding and swiping the steering wheel is manipulated to change the ship's direction. A mini-map in the bottom left corner shows the nearest missions or locations of interest. Tapping it brings up a larger, top-down map where the ship can be sent immediately to a new location if it has been discovered. New locations are uncovered on a global map when a certain level of experience has been reached and there are seven locations in total. The story is often furthered through conversations with static portraits of the characters.

There are different types of missions. In an assassination mission different types of ships need to be taken out. Those missions start with a top-down mini-game where the ship needs to be steered across a glowing green path while avoiding enemy vessels moving up and down the screen, to remain undetected. If detected, one or more ships need to be defeated first before the target is reached. Battles usually have a time limit and are in real-time. An icon on each side of the screen is used to dodge incoming shots. Attacking is done by determining the trajectory path along with two types of attacks: one with full cannons followed up with a precision shots when successful, similar to the combat in Black Flag. Both weapons and dodge have a cooldown time, also for the enemy attacks, so attacking has to be done strategically. It is also possible to zoom out and fire the swivel guns for a breaking attack. After a successful fight the player is rewarded with experience, money and different types of loot such as wood and books. Other types of missions include boat races, rescuing sailors, hunting down treasure based on maps and mystery missions. Most of them have primary and secondary objectives. Certain locations have treasure that needs to be located using a spyglass.

By leveling up additional crew members can be recruited from a tavern. Members also unlock additional perks for the ships. Perks are divided between active and passive abilities with a limited amount of slots. Passive ones determine the sail and the hull, while the active ones are the figurehead (certain power-ups such as speed boost) and the cannons. Perks can also be upgraded. There are different types of ships such as gun boats, schooners and brigs with statistics based on power, defense and speed. Ships can also be upgraded, but there is a maximum level for each of ship and certain ships can only be accessed when a certain level of experience has been reached. The game is entirely in 3D and both wind and weather influence the ship's maneuverability.

Updates to the game introduce whale hunting, collecting 50 species of fish, new ships, historical bosses, a survival mode, and a new playground environment with additional missions.

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