The Dark Island Trilogy is a set of three graphic novels that take place after the events of Skybound. Wu is the focus character, Clouse served as the main antagonist, and the Sky Pirates and the Shadow Army served as the villianous factions.
- 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; sometime 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 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 victoriously. 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. . . .
- In the early stage, Tommy Andreasen, Tommy Kalmar, and Kenneth Bonde spent a day at Andreasen's house brainstorming the ideas for the trilogy. They wanted to explore underutilized elements from the TV series and tie in components from Skybound and "Day of the Departed," the two adjacent TV installments. Greg Farshtey, the author of the series, stated how this was different than his other writing roles and was more akin to writing a movie novelization, because it was a story someone else had already come up with.
- Despite never being directly mentioned in the series, the events of the novels are considered by the writers to have a more significant role in Ninjago's history than "Day of the Departed," as the latter did not receive a mural and was not seen in the intro of March of the Oni, unlike the book series.
- This is the first time where Wu serves as the primary protagonist.
- The Golden Mech makes its first appearance since "Rise of the Spinjitzu Master."
- The Sky Pirates all return, none of which remember the events of Skybound, as the events were erased in "The Way Back."
- All of the Sky Pirates are incarcerated in Kryptarium Prison by the end of Part 3.
- Clouse is banished to the Underworld.
- The Ultra Stealth Raider, Rock Roader and Tumbler all make their first appearances in Part 2, revealed to have been built by Monkey Wretch.
- These novels also mark the first appearance of Ronin's Salvage M.E.C. and his new appearance.
- Wu has visions of both "Day of the Departed" and The Hands of Time, seeing all resurrected villains, Master Yang, Krux, Acronix, Ray, and Maya.
- Each book in the series has two season recaps at the end of the novel.
- The events of the three novels take place over the course of 32 days.
- Similarly to the Ninjago: Decoded, the trilogy starts with an unknown villain who is ultimately revealed to be a villain the ninja have previously fought.
- There will likely not be similar book series in the future due to the poor distribution of this trilogy. This led to the halt in production of another story, Amber Legacy, which would have explained the backstory of Skylor's mother.
- According to Tommy Kalmar, Rex Ogle from Little, Brown was the writer for Wu's journal.
- The story was partly inspired by the Mad Max franchise, specifically Mad Max: Fury Road, being described by Kalmar as "Ninjago meets Mad Max." This is especially prominent with Kai's story line in the desert in Part 3. Additionally, Apocalypse Now served as an unintentional inspiration, specifically for Wu journeying down the River of Darkness in the Destiny's Bounty.
- The events of this trilogy, specifically Jay and Nya encountering Misako and Ronin, is mentioned by Jay when assuring the other Ninja that Ronin can be trusted.