- For the location, see The Dark Island.
The Dark Island Trilogy is a set of three graphic novels that take place after the events of Season 6: Skybound.
- Main article: Dark Island Trilogy, Part 1
After investigating the Dark Island following the disappearance of several sailors, Misako and Ronin are attacked by pirates in the midst of a storm; some time later, their boat washes up back in Ninjago. Wu, who has been meditating for some time and sensing a growing threat, quickly assembles the six ninja to take the Destiny's Bounty 2.0 in search of them, bringing along a mysterious crate in the process. Unfortunately, the group is caught in a storm on the way to the island that scatters them, with Kai waking up in what appears to be a vast desert. Wu wakes up and finds the Bounty damaged nearby, only for Lloyd to appear being chased by a group of angry gorillas. After eluding them, uncle and nephew get the Bounty seaworthy and begin sailing upriver, with Wu noting that the influence of Dark Matter appears to be growing stronger all around them in his journal entries.
Elsewhere, Jay and Nya awake at No Man's Bluff and find their communicators inactive, and so begin searching for the others. They soon come across an unexpected sight: the pirates who attacked Misako and Ronin, who happen to be members of Nadakhan's crew, though only Jay and Nya remember the events of their previous encounters due to Jay's wish. The pirates have captured Ronin, who reveals that he was forced off their ship only for it to disappear along with Misako. As the ninja and pirates battle, The Leviathan appears and grabs Ronin, and Nya orders Jay to stop the pirates while she deals with it; however, he helps free Ronin instead, and the thief unveils his new Mech and aids the Nya in driving off the sea beast. The trio then set off to find Misako.
- Main article: Dark Island Trilogy, Part 2
Lloyd and Wu continued their journey up the River of Darkness, only to notice the effects of the Dark Matter upon the environment and be affected by it themselves, with Lloyd abusing his powers before taking off alone in search of Misako. Wu is similarly affected, with an insect bite causing him to envision a dark copy of himself who taunts him for using the Ninja for his own gains; however, Wu is able to banish this illusion. Meanwhile, Zane and Cole awaken and, after encountering a large bird, find a mine where Misako and the captured fishermen are being forced to dig up dark matter. An enraged Lloyd arrives and begins attacking, but Zane and Cole are able to calm him down before going after Misako, who has fallen under the influence of the dark matter but is purified by Lloyd's Energy.
The Sky Pirates mass for another attack, but the three ninja and the freed prisoners are aided by the arrival of Ronin, Nya, and Jay. Elsewhere, Wu discovers that the villain behind the troubles on Dark Island is none other than Clouse, who had come to the island after failing to acquire the Teapot of Tyrahn (due to Jay's final wish to Nadakhan). Having used his magic to forcibly recruit Nadakhan's crew, Clouse now seeks to use the Dark Matter to corrupt the Temple of Light, which will reunite the Dark Island and Ninjago as a landmass of darkness that Clouse will control. Clouse escapes Wu aboard Misfortune's Keep, while the Ninja acquire new vehicles created by Monkey Wretch and purified by their elemental energy. Cole then discovers Wu but is sent to search for the missing Kai.
- Main article: Dark Island Trilogy, Part 3
Kai, who has been wandering lost in the Billy Badlands, is captured by a pair of pirates but rescued by Cole, whose partial immunity to the Dark Matter enables him to reason with a partially corrupted Kai. The pair acquire new vehicles and set out to meet with the other ninja, eventually succeeding in doing so and making their way towards the Temple of Light. Unfortunately, the final convoy of Dark Matter needed to overwhelm the Temple of Light's defenses and corrupt it is already in motion, and the Dark Island itself is falling into chaos as a result of the evil energies. The ninja team reunites and attempts to stop the convoy, only to be attacked by Clouse and nearly buried under a magical sandstorm. Undeterred, the heroes make their way to the Temple of Light, determined to stop Clouse or die trying.
Upon arriving at the temple, the Ninja find that Clouse's plan is already well underway and are forced to confront his Shadow Army and Sky Pirates. Defeat seems inevitable, but Wu arrives and reveals the contents of his crate: his father's Golden Mech, which he soon pilots into battle against Clouse. Clouse responds by creating his own Shadow Mech from the members of his army, and the two engage in battle only for Wu to emerge victorious. The merging of Ninjago and the Dark Island is halted, the Temple of Light is restored to its original glory, and a vortex draws Clouse-unwilling to accept help from his enemies-into the Underworld. With the Sky Pirates captured and the balance restored for the time being, the Ninja celebrate their victory.
However, after returning to Ninjago, Wu notes in his journal that he senses another threat on the horizon: something involving Kai and Nya's mother and father and two twins he believed were lost to time...