Darkwing tells a tale of an ancestor from years ago named Darkwing Doubloon. The scene cuts to the royal family's ship with Seaman Drake handling the ship for the royal family a.k.a. the Muddlefoots. The ship is attacked by Negaduck and his pirate gang which includes Megavolt, Liquidator, Quackerjack, and Bushroot. They take the royal jewels and Negaduck tells them that he is a better pirate than the infamous Darkwing Doubloon.
After the pirates have left, Drake tells the Muddlefoots that the ship is sinking and that he will go down with the ship while they get away on a lifeboat. It was all just a ruse so Drake could become Darkwing Doubloon and use the ship. He gets his crew, which includes Gosalyn, Launchpad, Gizmoduck, and Stegmutt. They set sail to find Negaduck and retrieve the jewels. They find them and board Negaduck's ship. As they are fighting, Gosalyn goes into Negaduck's quarters and takes the treasure and hands it out to the crew a little at the time and they sneak it back to their ship. Just as she hands the last of it to Stegmutt, she gets trapped in the chest and locked in. Darkwing acts as if he has been beaten and is thrown overboard.
Back on the ship Darkwing realizes that Gosalyn is not there and knows that he must get her back. Gosalyn is discovered by Negaduck and he uses her as bait. Darkwing catches up to Negaduck and trades the treasure for Gosalyn who has secretly stolen Negaduck's map to his island. They are tricked and Negaduck sinks their ship and gets the treasure. Darkwing thinks that all is lost but Gosalyn tells him that he should not give up and they use Stegmutt for a boat and Gizmoduck provides propulsion and they use a map that Gosalyn stole to find Negaduck's island hideout.
Negaduck and his crew make it to the island and are bringing the treasure into his cave. They are ambushed one by one until Negaduck is the last one standing. He and Darkwing face off and Darkwing is triumphant.
Drake returns Negaduck's ship and the treasure to the royal family with Negaduck and his crew as prisoners. Negaduck threatens Drake and Drake threatens to call in Darkwing. Negaduck's crew tells him to shut up.