Investigating reports of sailors disappearing off the coast of the Dark Island, Misako and Ronin are themselves attacked and captured by pirates; a message from Misako warning Wu not to come looking for them soon reaches him, but he and the Ninja set out to find their friends regardless. The Destiny's Bounty is brought down in a storm on the way there, scattering the Ninja across the Dark Island; Jay and Nya end up locating Ronin in the captivity of the Sky Pirates, Nadakhan's crew. Perplexed as to the presence of the pirates, they work alongside Ronin to defeat them and a Leviathan that attacks them under the influence of Dark Matter, which seems to be affecting the entire landmass. Meanwhile, Wu and Lloyd awaken and begin sailing inland aboard the damaged Bounty, while the evil energies begin to affect them as well.
Lloyd, falling under the influence of the Dark Matter, leaves Wu to search for his mother, while Wu is forced to confront a specter that accuses him of using the Ninja for his own ends. Elsewhere, Zane and Cole awake and end up locating a mine where the Sky Pirates are forcing their captives-Misako included-to mine Dark Matter, only for it to fall under attack from an enraged Lloyd. They are able to snap him out of his stupor, and he in turn is able to help a Dark Matter addled Misako; the group are then reunited with Jay, Nya, and Ronin, and commandeer pirate vehicles that form the components of the Ultra Stealth Raider. Wu then discovers that the villain behind events on the Dark Island is Clouse, who intends to corrupt the Temple of Light with Dark Matter so as to reunite the Dark Island with Ninjago and rule over both. After he escapes aboard Misfortune's Keep, Wu is found by Cole, who instructs him to find the still missing Kai.
After being captured by pirates, Kai is freed by Cole and then freed from a Dark Matter induced rage, which Cole is resistant to due to his ghostly nature; the pair then join their friends in attacking a convoy transporting Dark Matter to the Temple of Light. Clouse attacks them in retaliation, and buries their vehicles before proceeding to the temple. The Ninja follow him and are reunited with Wu, but forced to deal with the Sky Pirates and Clouse's Shadow Army while Wu readies his secret weapon: his father's Golden Mech. In response, Clouse reshapes his shadows into a dark copy of the mech and battles Wu, but is defeated, allowing Wu to reinvigorate the temple and restore the balance, saving both Ninjago and the Dark Island from catastrophe. Clouse is drawn into the Underworld via a vortex created by this event, and the Sky Pirates are then restrained in preparation to have them incarcerated back in Ninjago.