The Protagonist is the played character in Sid Meier's Pirates! He is not directly named in-game during any cut scene, however the name Incognito prompts up during the name creation portion before the game play begins and it is assumed that this is his actual name. The player can change this name to whatever they like.
The story begins with the young boy at dinner with his family, celebrating that the debt they had owed was finally about to be paid off on the morrow. However, they are interrupted by the main antagonist, the Marquis de la Montalban, and a group of mercenaries. The Spaniard claims that the ship that had carried the debt payment has been lost at sea. The young boy runs away from the home, after the Montalban decides to capture his family, swearing to save them and avenge their abduction. Ten years later, the boy now an eighteen year old man, signs up with one of four captains, one from each nation to board a vessel and begin his journey. Now on board, the protagonist works as sailor for the ship. Having grown tired and sick of his captain's treatment, the man revolts and the ship goes into mutiny. After defeating his own captain, the crew elects the player as the new captain of the ship, and they send the old one off one a rowing boat with two other crew members who were most likely unwilling to follow their new captain. Now with a ship at his command and a family in heart, the player begins their quest to choose their path as a pirate.
The protagonist has brown hair made into a ponytail, and blue eyes. He wears a white shirt with a brown strap around his chest, a blue waist cloth, and tan-like pants, with light-brown boots. He changes his shirt based on what nation he is currently visiting, either yellow, blue, red, or orange, for Spanish, French, English, or Dutch, respectively. As the player gains rank with each nation, they get a visible upgrade that is added to their colored shirts, whether it be medals or straps.
As time moves on, the player becomes visibly older as he begins to gain wrinkles on his face. His age becomes more distinguishable for every three years that pass during the course of the game. Alongside this age change, his health also begins to diminish which causes slower movement speed during sword duels.
Depending on the player's actions and fame, after the plunder is divided, and the player chooses to retire, they are met with a score screen which denotes the status of the protagonists life in his remaining years and his retirement job. A short description is met changing depending on whether the player saved his family, avenged his family, whom he did or did not marry and gold and land acres accumulated.