After the events of Skybound, a new darkness threatens the Ninjago universe. While on a mission to find Misako and Ronin, a monstrous storm trashes the Destiny's Bounty, scattering the ninja across the Dark Island. Each must try to survive against impossible odds as they search for their friends before it's too late.
As Wu and the ninja journey across the sinister island, they'll be faced with new and old threats alike. Will their Spinjitzu and mastery over the elements be enough to stop the end of the world?
While sailing across the River of Darkness to the Temple of Light, Lloyd and Master Wu are attacked by a swarm of bees, now made aggressive by the corruptive influence of the Dark Matter on the island. Lloyd, likewise influenced, attacks the swarm, scaring them off. Despite Wu's concern over his heightened aggression, Lloyd brushes the incident aside, declaring his power as the Green Ninja as enough justification for his actions and stressing the need to find Misako.
Continuing their voyage on the Destiny's Bounty, Lloyd quickly grows impatient, and despite Wu's attempts to assuage his anger, leaves his uncle to rescue his mother and friends. Desperate to end the source of Dark Matter as quickly as possible, Wu chooses to leave Lloyd in his search and arrive at the Temple of Light.
Meanwhile, Zane, recovering from the crash on the snowy peaks of the dark island, wakes up to find his friend Cole. Before the two can discuss, however, they're swooped up by a massive eagle and flown towards a nearby volcano. Using the beast as unorthodox transport, the two free themselves upon approaching land and find themselves near a mine operated by the kidnapped fishermen, including Misako, now being supervised by the Sky Pirates.
With horror, the two realize the fishermen are mining Dark Matter, and witness an aggressive Lloyd attack the mines, defeating the Sky Pirate sentries. Confronting their friend, the two manage to snap Lloyd out of his vengeful trance, and the two head further into the mines to save Misako as well. However, they discover that Misako has likewise been influenced by the darkness and is dedicated to her cause, even as Dogshank and other Sky Pirates, alerted by Lloyd's mother, come in to detain the trio. Engaging in combat, Lloyd defeats Dogshank using his powers over Energy, inadvertently freeing Misako from the dark matter's influence. Realizing that Elemental Energy is able to nullify and cleanse the affects of Dark Matter, Misako and Lloyd head off to free the rest of the prisoners while Cole and Zane find transportation.
Traversing the mines, Cole and Zane come across Monkey Wretch, and interrogating him in exchange for the Sky Pirate's safety, find out that he's created vehicles powered by Dark Matter and will take them to the rest of his crew. Leading to the two outside of the mines, Monkey Wretch presents his latest creations, the Titanium Ninja Tumbler and Ultra Stealth Raider, both powered by Dark Matter.
As Cole and Zane discuss their new vehicles, they're quickly encountered by Jay, Nya, and Ronin, who assist them in boarding the vehicles, discovering that their elemental power is able to cleanse the dark matter and power the machines instead. Driving off, they encounter Misako and Lloyd, having freed the rest of the prisoners, only for the Sky Pirates to return. With the additional reinforcement of Monkey Wretch's vehicles, the ninja are able to force the Sky Pirates into retreat, with Flintlocke gloating that their victory won't last and expressing plans to regroup with their master at the Temple of Light.
Even as the rescued fishermen make plans to salvage the abandoned Sky Pirate boats and sail home, the Ninja make course, following the trail of the Sky Pirates to the Temple of Light. Meanwhile, Wu, recording his growing insanity and corruption in his journal, succeeds in meditating his ill thoughts away. However, infected by a Dark Matter plagued mosquito, Wu receives a malevolent vision of a shadow version of him, which goads him towards the darkness. At first surprised, Wu remains undeterred and shrugs off the hallucination, arriving at a dark cave.
Meanwhile, traveling in their vehicles, Jay, Nya, Ronin, and the others discuss the whereabouts of Kai and Wu. With Monkey Wretch now riding alongside and assisting the team, the mechanical primate informs them that the Ultra Stealth Raider can split into multiple vehicles, and under Lloyd's orders, Cole flies off in the Ultra Stealth Raider's jet to find Wu, likewise noting his ghostly status grants minor immunity to the dark influence.
Elsewhere, exploring the caverns, Wu discovers Clouse, still a ghost after having his mortality revoked by Jay's last wish. Combating Clouse, Wu is quickly ensnared in chains of dark energy, even as Clouse gloats. Revealing how he escaped his cell within the Preeminent after Morro unleashed the Cursed Realm upon Stiix, Clouse, frustrated by his failure in retrieving the Teapot of Tyrahn, instead sought a new way to restore his power through the dark energies of the Island of Darkness. Succeeding, Clouse used his Magic to bring back the Sky Pirates from the Sixteen Realms. Threatening to banish them again should they not obey him, Clouse set them to work kidnapping fishermen as a workforce for mining the inert troves of Dark Matter on the island left undisturbed.
Triumphant, Clouse explains his plot saying that the Temple of Light as the source of light and good for the Island of Darkness, he intends to assault its defenses with countless amounts of Dark Matter, eventually overwhelming and corrupting the structure. With the single source of light now turned dark, both the Dark Island and Ninjago will be corrupted, with Clouse at its control.
Wu, reprimanding Clouse's foolishness and warning him that his actions could potentially destroy the Sixteen Realms, laments how he could've been an agent of good, but Clouse, too far gone, ignores Wu's warnings and gloats over his anticipated victory over the Ninja. Wu, having heard enough, breaks free of his bonds and attacks. Clouse, deciding the battle to be pointless, summons the once again upgraded Misfortune's Keep, animated by his magic, to transport him away to the Temple of Light.
Cole eventually discovers Wu, who orders him to find the lost Kai and thus restore the entire team. Even as Cole flies off, Wu ponders his impending destiny and notes his secret cargo on board the Destiny's Bounty, a cargo that once helped the First Spinjitzu Master save the world. Reminding himself not to dare let anyone know of its nature, Wu returns to his journey.