A factory in Ninjago Village is under siege by an unstoppable new menace, with the beloved mayor and his daughter held hostage! Only Nya, Jay, Cole, Zane, and Kai — the Masters of Spinjitzu — can save the day . . . or can they? Much to the brave warriors’ astonishment, a new gray ninja is on the scene! Is the Phantom Ninja friend or foe, and will his reckless fighting style sabotage the rescue mission before it even starts?
While patrolling Nom, two Nindroid Drones are attacked and subdued by a mysterious Phantom Ninja that appears through a cloud of smoke. Meanwhile, in a nearby campfire, the Ninja team discuss what the Overlord is planning, only for Jay to arrive, indicating the presence of the Nindroids in the nearby village.
Investigating, the ninja realize that the Nindroids have taken the citizens hostage, forcing them to create more Nindroids in the factory. Formulating a plan, Nya visits the village the next day, pretending to be a traveler looking for work. From the citizens, she learns that the Nindroids are expecting a shipment of raw metals that night.
Hiding in the woods that night, the ninja encounter the truck delivering the metal, only for the Phantom Ninja to arrive, piercing the engine and making plans to take revenge on the truck driver for his involvement, regardless of his knowledge of the Nindroids or not. However, the Ninja intervene, allowing the driver to escape, and the Phantom Ninja leaves, warning the ninja not to get in the way of its vengeance.
The next day, the ninja discuss the Phantom Ninja and the idea of the villagers being forced to work for the Nindroids. That night, Jay, theorizing that the Phantom Ninja is actually a Nindroid trying to trick them, confronts the enigmatic warrior atop one of the roofs. After using a magnet to deduce whether or not the Phantom Ninja is a Nindroid, leading to Jay's shock over his theory being disproven, he and the Phantom Ninja get into a brief scuffle. Ultimately, Nya arrives to intervene, and the Phantom Ninja escapes.
The next day, the ninja sneak into the village, gaining the cooperation of Eve, who manages to convince her father to explain how the Nindroids first took over Nom. Though wary, the father agrees, explaining how the Nindroids attacked in the dead of night, taking the mayor and his daughter, Seliel, hostage. However, soon after employing the village to create machines for them, the Phantom Ninja appeared, its arrival being signified by a cloud of smoke, before taking vengeance on Nindroids and disappearing.
Zane, from the story, theorizes the identity of the Phantom Ninja, and the ninja make plans. Nya heads out to find the mayor and Seliel, and arriving near the factory, the only place where the prisoners could be, spots something that shocks her enormously. Meanwhile, Kai and Jay, seeking to destroy the power as part of the plan, fight off the security system, which disguises itself as inanimate cables. Even as Cole dresses Zane up as a Nindroid, Nya is captured by several Nindroids, who discuss killing her immediately.
At the factory, the power goes out, and Zane, disguised, orders that the villagers leave and move to New Ninjago City, successfully getting them to escape. However, trouble arises when the Phantom Ninja appears, causing chaos, even as the Nindroids see through Zane's disguise. With the help of Cole, Jay, and Kai, they manage to fend off the Nindroids, even as Nya escapes her captors.
The Phantom Ninja takes its leave, disappearing, even as the ninja escape, deciding their next action is to ensure that the Phantom Ninja is on their side, or at the very least, stops interfering. The next night, Cole encounters the Phantom Ninja exiting out of the side of the factory, exposing it as Seliel, the mayor's daughter. Revealing her supernatural smoke was nothing more than smoke pellets, Cole is attacked by a hostile Seliel, but manages to subdue and negotiate with her. With her village in danger, Seliel ultimately decides to accept the help of the ninja, getting over her anger over their initial absence.
The next day, the Ninja prepare their final phase of their plan, before Seliel lures General Cryptor and the rest of the Nindroids to the North Woods that night. As the nindroids explore the forest, in search of the villagers, the ninja ambush them with the various traps they had set up. Despite their victory, Cryptor gloats that he'll take vengeance on the Mayor and Seliel, only for Seliel to reveal herself, having rescued her father in the chaos. Defeated, Cryptor escapes.
Even as the protagonists reconcile, Seliel explains how, after seeing the ninja fight the Skulkin some time ago, she became inspired to become a ninja herself, training everyday and inventing her smoke pellets. Before she could begin her adventures, however, the Nindroids captured Seliel and her father, holding them prisoner. Luckily, Seliel managed to discover an exit one night while her father slept, but, fearing her father's fate should he be recaptured, chose not to tell him and would regularly leave the factory every night to fight the Nindroids as the Phantom Ninja.
However, despite their apparent success, Seliel reveals that the Nindroid parts that were being manufactured were useless, hollow pieces. Cole comes to the conclusion that the Overlord had taken over Nom Village simply to distract the ninja while he worked on his real plan. Nevertheless, Seliel and her father thank the ninja for their help and take their leave, offering her help in the future.
Days later, while observing the constellations, Seliel manages to get her father's approval to become the Phantom Ninja. Even as she reminisces on her next encounter with the ninja, she stares into the sky at the comet Arcturus, where, unbeknownst to her, the ninja are currently fighting the shape-shifting alien.
- Tommy Andreasen has stated that the graphic novel can be considered canon since it does not contradict anything in the show.
- The graphic novel marks the debut of Seliel.
- The novel marks the second appearance of a Phantom Ninja, the first being in Cole: Ninja of Earth. Despite the two characters' status as anti-heroes who leave their identities unknown, the two are unrelated.
- The story seems to take place between the events of "Enter the Digiverse" and "Codename: Arcturus," as the Ninja constantly refer to a secret plan that the Overlord is working on.
- There is a panel in which Jay flirts with the phantom, prompting jealousy from Nya.
The images on Who is the Phantom Ninja? need to be organized.