John Fletcher was the father of Jack Fletcher and the pilot of the Alexandria. When the Wakou attacked, the Ninja Dragon Eye ran him through and mortally wounded him when he was trying to defend Jack. With his last breath, he told his son to find the rutter, as it will get him home. His body is assumed lost to sea after the Alexandria explodes.
John Fletcher had taught his son the skills needed to be an efficient navigator and pilot, in addition to his existing skillset as a rigging monkey on-board ship. Though he is dead, Jack still thinks of him many times as spiritual comfort, and to strengthen his will in getting back to England safely.