Unlike most of the Hanna-Barbera cartoons, The Pirates of Dark Water used a serial story line that progressed from one episode to the next. As such, the series had a back story that guided much of what the characters did.
On the alien world of Mer, teenager Ren began his adventure on the day he found a man washed ashore near the lighthouse he attended. The man turned out to be King Primus of Octopon, who had disappeared 17 years earlier around the time his kingdom was destroyed. The king also revealed that Ren was his son, who had been but an infant at the time of the disaster.
Primus’ disappearance lay in the serious threat posed to Mer’s vast oceans. A roving substance known as Dark Water devoured whatever it came into contact with. It originated from the core of the planet in a place ruled by an evil specter known as the Dark Dweller. For eons no one could leave this domain of darkness due to the Thirteen Treasures of Rule which served as a protective seal. Then the Dark Dweller caused a rift in the ocean bed, which began the scourge of Dark Water. Immediately the Dark Dweller sent his chief servant Keroptus to seize the thirteen treasures and scatter them across Mer so that the Dark Water could not be stopped.
Sometime after this event, King Primus learned of the lost treasures and with a crew of loyal followers set sail to find them in order to save his world. After successfully gathering the first seven, his crew crossed paths with the evil pirate lord Bloth, who wanted the treasures for himself so that he could control the Dark Water, and thus all of Mer. Primus gave the seven treasures to his most trusted captains before he was captured. His captains escaped and hid the treasures, after which Bloth burned Octopon to the ground in search of them.
After 17 years in captivity Primus was able to escape and seek out Ren, his only surviving heir, who accepted his father’s dying charge to reclaim the treasures. Ren soon gathered an unlikely crew to assist him in his journey: a greedy and opportunistic pirate named Ioz, a headstrong ecomancer with many secrets named Tula, and a perpetually hungry monkey-bird named Niddler. Aboard a swift vessel called The Wraith, Ren and crew faced the adventures of finding lost treasures with the persistent menace of Bloth at their back, aboard his massive warship The Maelstrom with its deadly crew.
The series had an irregular television run. A five-part mini-series aired on Fox Kids in 1991 titled Dark Water. After some minor changes to the animation and voice actor work, those episodes were rebroadcast later in 1991 on ABC as the first five episodes of the regular series, which included eight new episodes. An additional eight episodes were produced for the second season, which aired in first-run syndication as part of The Funtastic World of Hanna-Barbera. Although the story line never officially concluded, the series was cancelled after its second season.