Captain Hook is sailing through a storm and facing sea monsters. However, it turns out to be a nightmare. The Jolly Roger crew is following the Bucky crew to the Mighty Colossus shipwreck and its treasure. After sending them packing, Hook looks for the Mighty Colossus but soon concludes that it's a wild goose chase. However, he accidentally frees the evil merwizard, Lord Fathom who heads for Neptune City, where he tricks Queen Coralie into helping him get the Darklight Emerald and then imprisons her, Marina, and Stormy and takes over Neptune City.
Sandy tells Jake and his friends what happened while Fathom places all the sea creatures in the Never Sea under his control. The Bucky crew head to Neptune City while Fathom heads toward Dreadnought Cove. Thanks to Hook, Jake and Fathom run into each other. Before sending them flying, he reveals he intends to unleash the Strake, the most ferocious monster in the Never Sea. Cubby realizes they can't defeat Lord Fathom on their own so Jake decided they need more help from the Captains of Neverland and he sends Skully to tell the captains to report to Neverland Beach for an emergency meeting. To deal with this new threat, Jake creates the League of Never Sea Captains: himself, Captain Hook, Captain Flynn, Captain Frost, and Beatrice Le Beak. The League tries to stop Lord Fathom, but he's far too powerful so Jake decided they need to retreat and hide somewhere where Lord Fathom won't find them to think of another plan. Jake's sword suddenly makes the Mighty Colossus rise out of the water and makes him its captain and they set off to fight the mer-wizard.
Meanwhile, Lord Fathom releases the Strake and places it under his control and a battle erupts. King Neptune appears and tells Jake that all he needs to defeat Fathom and the Strake is to believe in himself. Using the powers of his sword, Jake finally defeats Fathom and the Strake. He then reimprisons the Strake and destroys the Darklight Emerald, freeing Queen Coralie, Marina, Stormy, and the sea creatures who send Fathom packing.
- A book of this episode came out June 23, 2015, according to Amazon.com.
- This is the fourth 1-hour special ("Jake and the Never Land Pirates: Peter Pan Returns", "Jake and the Never Land Pirates: Never Land Rescue", "Jake and the Never Land Pirates: Battle for the Book"), and eighth episode that is longer than 11 minutes (the 4 mentioned, "Pirate Genie-in-a-Bottle!", "Jake's Royal Rescue", "Pirate Genie Tales", and "Smee-erella").
- This is also be the first special to not be marketed as a "Family Night Special Event", as it will air during the day as part of Disney Junior's Soaring Over Summer promotion.
- This is the second special episode to not feature any gold doubloons ( the first being "Battle for the Book").
- This special episode marks Jake's official captain status.