Tommy Klopt is cunning and clever. Of course, he's a pirate. The 12-year-old, along with his brothers, Connor and Dillon, begin a life at sea when their distraught father, Hoody, hits hard times. After a couple of years of smooth sailing as Robin Hood-type pirates, the family encounters a typhoon in the form of 400-year-old pirate ghost, Francois l'Olonnais. To force Tommy to complete a task, l'Olonnais captures Hoody. In a race against time to free him, the boys go up against real pirates and the FBI.
For two years, twelve-year-old Tommy Klopt, his dad, Hoody, and his two brothers, Connor and Dillon, sailed the seas as Robin Hood-type pirates. After meeting, and almost getting killed, by a pirate from the 1600s turned evil ghost, Francois l'Olonnais, the family decides to head back to land and start over.
Tommy Klopt and his family are starting fresh on the straight and narrow. With their new crew member, Cosette, who they saved from a sea witch, the Klopts are building a life in New England. The ever-present ghost pirate, Francois l'Olonnais, has grown quite a reputation in the ghostly realm since meeting the family. He's garnered respect for acquiring a new crew of mortals, the Klopt family, at his beck and call.
After the Klopt's square their debt with pirate ghost Jacques Mignard, they are left with a new crew member, Cosette, and a debt owed to a sea witch, Volange that brings them to Scotland. Pirate ghost François l'Olonnais, always with a watchful eye over Tommy, decides to lend the family a hand for their next quest. He enlists the help of a Scottish pirate ghost, Captain Red Boots. Working in a time crunch, with two new crew members that don't see eye to eye, and avoiding Volange's powerful brother who wants to stop them, the Klopt family is in for more than their share of rough seas.