The game is focused on a young and naive British Dachshund named Gaius James Rover who is sailing across the seas to deliver a cargo of Jolly Rover, a brew made of rum spoiled by tobacco to governor Guy DeSilver residing on Groggy Island, a small backwater and haven for pirates.

However, James is quickly captured by pirates led by Captain Howell who is the first one to give him the nickname and titular name Jolly Rover.

After three weeks in capture, James Rover manages to escape and disguises himself and meets Juan Leon the Parrot, a wisecracking animal sidekick that would serve as the hint system for the game progress.

DeSilver then proceeds to threaten a rather desperate and reluctant James to settle the debt of 50 pieces-of-eights by paying him 5 pieces per month or be put in jail and most likely hanged.

After Captain Silvereye mysteriously disappeared, DeSilver semi retired and became governor of Groggy Island, controlling the blackmarket trade with an iron fist.

James disguises and infiltrates the camp where he meets a female cocker spaniel and love interest Clara DeSilver, the daughter of Captain Silvereye.

The two team up to escape the island since Clara no longer desires to be with her previous crew and arrives to a labyrinth cave where her father's ship The Red Herring is hidden but none of them can really find it.

James uses the Raise the Dead spell and summons the spirit of Captain Silvereye who takes the ship to Shipwreck Island, Clara's family home.

James finally embraces his destiny as Jolly Rover the Pirate and challenges DeSilver... Only to get a sword handle delivered to his head which knocks him out.

But James manages to lure a sea turtle and ties it to the barrel with the rope and he runs off back to Groggy Island to save Clara from DeSilver and the voodoo priest.

", James throws one of his red balls on a very confused DeSilver who stumbles over the voodoo priest and they both fall over the cliff into a pit of hot boiling water.