The Sky Pirates are a crew of diverse goons that were brought together by their captain, Nadakhan, many years ago. Unlike many other villainous factions in Ninjago, the group contains an extremely wide variety of warriors, ranging from all sorts of sizes and looks. Initially seeking gold and profit, the Sky Pirates' intentions are changed to vengeance against the ninja and the reconstruction of Djinjago and domination of the skies.

Long ago, the Sky Pirates were marooned across the Sixteen Realms by Captain Soto, who also imprisoned Nadakhan in the Teapot of Tyrahn. After Clouse freed Nadakhan many years later, the deceptive Djinn reunited his crew and found out his home realm was collapsing. As a result, he sought vengeance of the ninja, trapping all of them in the Djinn Blade except Jay and Nya. Nadakhan tried marrying Nya to obtain infinite wishes, while Jay formed a rag-tag team to raid Djinjago.

The Sky Pirates fought against the ninja and their allies, cooperating with Nadakhan up until the wedding ceremony when his full ferocity was unveiled. Nadakhan turned against his crew, banishing several Sky Pirates to other realms, while Flintlocke and Dogshank helped the ninja weaken him with the Tiger Widow's venom. However, the venom also got on Nya, and she died. Jay then made his final wish, that Clouse never found the teapot—Nadakhan granted Jay's wish, undoing recent events and sending the Sky Pirates back to their respective realms.

Despite this initial defeat, however, the Sky Pirates would quickly be called into action once more by the very events of Jay's wish, ironically; with Clouse unable to retrieve the Teapot of Tyrahn in the reset timeline, the sorcerer instead traveled to the Dark Island as an alternate source to restore his magic. Rejuvenated by the sinister energies, Clouse was able to summon the Sky Pirates from their realms, and threatening to banish them again, forced them into his service, having them kidnap fishermen on the Endless Sea under the cover of storms to use as a slave force mining Dark Matter. Participating in these kidnappings, the Sky Pirates' exploits in helping Clouse retrieve the substance needed to corrupt the Temple of Light eventually attracted the attention of the ninja once more. After the battle, the Sky Pirates were all sent to Kryptarium Prison.