Season 6: Skybound

Nadakhan proceeds to frame the Ninja, making them wanted criminals. The Ninja, in Stiix try to find Clouse, flee but are chased by the citizens, who are angry with them for destroying their town. Misako pilots the Destiny's Bounty to get them but ends up crashing down by the police. The Ninja manage to split up and escape but Misako gets arrested.

Earlier that day, Nadakhan finds Sensei Wu in the Domu library and hears him saying, "be careful what you wish for," and imprisoning him in the Teapot of Tyrahn. When Misako is left in a room handcuffed, Nadakhan comes and tricks Misako into telling him the secret location of the Realm Crystal and also imprisons her in his teapot.

Ronin is then hired by the Police Commissioner to find the Ninja and bring them to justice. While the Ninja split up into three teams of two, Jay and Cole discover that Nadakhan could shapeshift, explaining how he framed them. After Ronin cunningly captures all of the Ninja, they are brought to Kryptarium Prison. Meanwhile, Nadakhan goes to the location of the Realm Crystal in the Hiroshi Labyrinth Stronghold and steals it.

At Kryptarium Prison, the Ninja find Captain Soto and he tells them how to catch a Djinn, the answer being to use a drop of Tiger Widow venom to weaken Nadakhan. After freeing Soto and themselves, Captain Soto told them that the last Tiger Widow lived on an island not found on any map but in a lantern hidden on Misfortune's Keep.

Meanwhile, Nadakhan (who was once a pirate) freed his crew from different realms from which they were banished to.

The police was focused on finding the Ninja but unknown to them, Nya and Jay were disguised as policemen and had logged in to the police system searching for Nadhakan's ship but found nothing.

Meanwhile, Cole and Lloyd flew on their Elemental Dragons back to the last known location of Nadhakan's ship only to find electric wiring and other metal parts. Zane and Kai went to the crash site of the Destiny's Bountyonly to find the need to escape, leaving their ship behind.

Meanwhile, Nadakhan and his crew visit to his home realm, Djinjago, but it was slowly falling apart. Nadhakan's father, the Djinn King, told Nadakhan that the Sixteen Realms were all interconnected. When the Ninja destroyed the Cursed Realm, they also destroy Djinjago. Nadhakan's father gave him the Sword of Souls that had the power to hold life forces. Nadhakan then slashed the Teapot of Tyrahn with it, causing the souls of Clouse, Sensei Wu, and Misako to transfer inside the sword. He then returned to Njnjago and swore the Ninja would pay for their actions.

However, the Ninja learned much about the true enemy and got the only thing needed to stop him, though they were taken down by the Dijinn one by one. The pirates tries to break Jay through different methods after capturing him to make him use his final wish, but failed every time. Even after the rescue, both Jay and Nya were the only one left and went into hiding in order to organize their plans, though Jay was shaken over the loss of their comrades. During their last confrontation, Jay was pushed into the portal made by Travelers Tea and Nya was captured.

Jay gathers a team to help him to save his comrades, though he was unable to save Nya in time. Fortunately, Nya helped Jay to get the sword to save his friends and they crashed the wedding.

Jay manages to make a final wish that all of the events transpired should not happen in the first place, mourning over the loss of Nya. Due to the venom and the purity of the wish, Nadakhan gave Jay what he want by reversing time and return back to the point where everything started. As both Jay and Nya realizes that they were the only ones who remembered the events, both of them embraced and rekindled their relationship, much to the others' confusion over what happened. The reunion of the Lightning and Water Ninja was broadcast all over Ninjago by Dareth. At the same time, Clouse found the teapot, but this time got chased away by the citizens, which fortunately prevented the same events from happening again. At the same time, Yang's Haunted Temple was seen floating on the sky, marking a new future challenge against the Ninja.

Episodes:
55."Infamous"
56."Public Enemy Number One"
57."Enkrypted"
58.Misfortune Rising"
59.On a Wish and a Prayer"
60.My Dinner With Nadakhan
61"Wishmasters"
62.The Last Resort"
63.Operation Land Ho!"
64.The Way Back" (Season Finale)