In the wake of the Preeminent's defeat, the Ninja have become celebrities, but Nya is struggling with both her new status on the team and Jay's lingering feelings for her.
The Ninja soon have bigger things to worry about, however, as their old foe Clouse unleashes the villainous Djinn, Nadakhan, a wish-granting pirate who quickly captures Wu and Misako before setting out to locate his long-missing crew after framing the Ninja for a series of crimes that turns the populace against them.
After returning to his home realm of Djinjago only to find it falling apart; he then receives the Djinn Blade from his father and returns to Ninjago intent on reshaping it into a new version of his home. In an effort to halt him, the Ninja seek advice from Nadakhan's old foe Captain Soto, who advises them to seek out Tiger Widow Island for the means of weakening the Djinn.
The Ninja succeed in obtaining the venom of the Tiger Widow, but in the process Kai and Zane are trapped with Nadakhan's blade and their power enables him to lift pieces of Ninjago into the sky in his bid to recreate Djinjago.
At the same time, he seeks the hand of Nya—the double of his lost love Dilara—in order to gain the ability to grant himself infinite wishes. In the end, it is up to Jay—the only Ninja who hasn't used all three of the wishes Nadakhan can grant him—to assemble a team of reserve heroes to save his friends and stop Nadakhan from conquering Ninjago with infinite power.
In the end Jay was able to save Nya and all his friends. In all of this their was still no sign of Aria and they just had to wait longer for her return.