In the final battle against Jones and Cutler Beckett, Bootstrap, still delusional, fights Will without recognizing him. He is subdued by Will, and only recognises his son after seeing Jones stab him. In a fit of rage, Bootstrap attacks Jones, allowing Will to kill him. With their captain gone, Bootstrap and the other crewmen cut out Will's heart and place it in the Dead Man's Chest, making him the new captain of "Flying Dutchman". Following the battle's end, Will offers his father the chance to leave the ship and live a normal life, but Bootstrap, desiring to make up for having abandoned Will when he was a boy, chooses to stay with his son aboard "Flying Dutchman".