The series opens on Jim Hawkins as an adult, a doctor on an English ship stopped in the bay of an island. The captain shows Jim a grave he found of a pirate, Long John Silver. Jim remembers this old friend Long John. He starts to tell the captain of his past adventures sailing with him.
Jim and his mother are homeless and without work. On the intercession of the good Dr. Livesey, Squire Trelawney welcomes them to his property. Jim shows them the map leading to the treasure of Captain Flint.
Together they set sail for Bristol. On the ship Silver teaches Jim small lessons of easy seafaring. Meanwhile, Shadow keeps a close eye on the navigation of the Hispaniola thanks to his spy and a traveler-raven that keeps them in contact.
Jim discovers the truth about Long John and his secret agenda. Jim tries to warn Captain Smollett of the pirates and their plans of mutiny.
Jim and his friends go to save JoJo from the pirates. However, the pirates spot them before they can run away. They are saved by a man hidden in the forest.
Jim and his friends are fugitives running from Governor Blade and Shadow as well as zombies! Jim and friends take back control of the ship.
Jim, friends and Silver attempt to flee from Jamaica. Governor Blade is on a search for all of them. The fugitives hide out in the palace.
Jim and friends manage to escape the governor and all his men. Silver wants to guide them to Tortuga, a safe haven for pirates.
They depart from the island of Tortuga. Jim enters a life he is not prepared for. But Jim might just have what it takes to be a true Captain.
Blade is planning to attach with zombies. JoJo knows regular weapons won't be enough to defeat them.
Blade's true identity is revealed. Jim and crew continue to flee. Long John leads them to a secret passage where they may rest.
Guided by JoJo, they search for his mother Kainda, who will help them defeat the zombies. However, Shadow has his own plans that will lead him to Africa as well.
Shadow takes on an old enemy and tries to make a deal with Kainda. Ben is anxious about all that is happening and may know more than it seems.
Long John leads Jim and friends on an escape. Meanwhile, Governor Blade is acting increasingly strange and angry.
Jim and crew find Kainda. With her magic, they will now be able to fight the zombies.
Devastated, JoJo goes to search for Mama Kainda's body in the water. Jim follows but soon after, both must retreat to the ship. Blade and Shadow are close on their tail. Jim spots a wandering zombie and decides they must capture him to warn the rest of the world.
Half of the crew ventures onto the island to capture the zombie. Meanwhile the ship and the rest of the crew are hiding from Blade. Jim and friends must conquer quicksand and other obstacles of the tropical forest to get the wandering zombie to the ship.
Jim and crew sail for Veracruz to reveal the zombie to the authorities. Shadow sends out his ravens to locate Jim's ship. Flint is injured.
Jim wants to return to Veracruz to retrieve the Codex. The crew is nervous for Jim but aids him in preparation for his plan. Jim and Flint are on their own.
Jim retrieved the Codex and returned to his friends. Soon after, Jim and crew run into Pirates from different parts of the world all out for the feat of the Great Golden fleet, the largest shipment of gold in history. Jim and Silver think it is a trap.
Governor Blade has rallied his allied fleets to declare war on the Pirates. The Chinese Pirates are the only ones that believe Jim and his friends about the impending doom. They gift Tracy a brand new ship. They are ready for the challenge.
Jim and crew must now fight many more zombies. JoJo is struggling to control his anger and hatred but Jim is going to help him. Meanwhile, Shadow has come across new knowledge to complete his evil grand plan.
Jim and crew search for Kainda. Huracan is getting closer to achieving his vengeance carried out by Blade.
Jim thinks they must travel to Skull Island. Ben is scared. Kainda helps reveal his knowledge of the island and Huracan to the others.
Jim wants to reach Huracan and convince him to stop his evil plan of revenge. Blade is determined to achieve vengeance for both Huracan and himself.
Skull Island is the location for the final challenge between good and evil, between Jim and friends and Flint/Blade with a crew of zombies. Who will prevail?