Now that they have destroyed the Cursed Realm and rescued Ninjago, the Ninjas are suddenly very famous. However, they must be careful what they wish for as a new era of piracy has begun with the release of a new evil known as Nadakhan the Djinn.
The Ninjas need to learn everything they can about Nadakhan before he locates the Realm Crystal. However, they get pursued by their former comrade Ronan after they are declared enemies by the world they were supposed to defend.
When the Ninjas get falsely imprisoned and are at their lowest, they unexpectedly make a friend out of an old foe. Nadakhan saves his trapped crew and learns a viewpoint and an intriguing new scheme.
The Ninjas are headed for a collision as they need to locate Nadakhan before they can locate the map that will stop him. Jay, in the meantime, wishes to change his future, but it might permanently change his past.
To use tiger widow spider venom against Nadakhan, the Ninjas journey to Tiger Widow Island. When Nadakhan shows up to step in and intervene, the plan goes south.
While the other ninjas make an effort to stay alive and flee Tiger Widow Island, Jay must do his best to escape the evil grasp of Nadakhan.
In a desperate attempt to rescue Jay and finally vanquish Nadakhan, the last remaining Ninjas take on the challenge of infiltrating the Sky Pirates.
The Sky Pirates learn where the two remaining Ninjas are kept safe and launch an assault to find the one who can unleash Azad's greatest potential.
The last surviving ninja daringly searches for the rest of his friends while enlisting the aid of old allies to prevent Nadakhan's wedding from happening.
Nya and Nadakhan's wedding takes place, although the rescued ninjas have tried their best to save her. All Jay has left is one final wish, which he must fulfill.