Following the destruction of the Cursed Realm and the ultimate death of all its prisoners, the Ninja have found sudden fame for their roles and actions. Yet, amid their newfound popularity, a new threat is posed when a survivor of the Cursed Realm's destruction, Clouse, loiters in Ninjago to wreak further havoc. The Ninja attempt to stop him, but they are ultimately subdued and unable to do so. Clouse heads to Stiix, where he finds the ancient Teapot of Tyrahn, which contains a deceptive Djinn named Nadakhan who imprisons Clouse in the teapot following his release. As the Ninja arrive in Stiix, they discover they have been framed for a series of crimes and are pursued by the city's inhabitants. In the meantime, Nadakhan finds out what has happened to his crew of Sky Pirates, and eventually captures Sensei Wu after accidentally being summoned by him. 

The Ninja are declared to be the Public Enemy Number One after being framed by Nadakhan for crimes they did not commit. Ronin offers to capture the Ninja in exchange for a 'clean slate,' meaning all of the crimes he committed, will be undone. Meanwhile, Misako is captured by Nadakhan. The Ninja devises a plan to separate into pairs so that they can't all be arrested. Ronin hacks into Zane's system and shuts him down, and then captures Lloyd. After Kai and Nya find out what happened to Zane and Lloyd, Ronin comes after them and tricks them into being caught. Jay and Cole go to Mega Monster Amusement Park, and Ronin chases around them around the park and finally captures them. The Ninja are then brought into custody. Nadakhan steals the Realm Crystal from a maze built by Cyrus Borg called Hiroshe's labyrinth. The Ninja are shipped it off to Kryptarium Prison. 

The Ninja get 'special treatment' at the Kryptarium Prison, and the Mechanic wants to use Zane for spare parts. Nadakhan brings his crew back from other realms: Flintlocke, Clancee, Doubloon, Monkey Wretch, and Dogshank. The Ninja start a food fight and befriend Soto, the captain who trapped Nadakhan into the Teapot of Tyrahn and told the Ninja how to stop Nadakhan: Tiger Widow venom, and bust themselves and Soto out of Kryptarium. Nadakhan visits the Kingdom of Djinjago realm and finds out that when the Ninja destroyed the Cursed Realm, this realm and kingdom started to collapse. He promised to avenge the people of his Realm and Kingdom. The Ninja find out that the map is in a lantern aboard the Misfortune's Keep. 

The Ninja are undercover in the Police Station. Nadakhan visits Jay, making him use his wishes, and he finds out that he was adopted. The Sky Pirates attack the city, and the Ninja try to stop them. Kai gets captured by Nadakhan, while the rest of the Ninja get the Lantern. The land gets stolen by the Sky Pirates to rebuild the Kingdom of Djinjago.

The other Ninja travel by boat to a dangerous island, but during the journey, there is a lightning storm, and Zane goes below deck and finds Nadakhan, who tricks Zane into wishing himself away. When the Ninja arrive, they wondered how Jay got a mansion and a stylish boat, so when Cole tells that he saw Nadakhan, the Ninja make Jay retrieve the Tiger Widow Venom, but when Nadakhan finds out that the Ninja is getting the only thing that can stop him, he ambushes the Ninja, but when Jay successfully gets the venom, Nadakhan teleported to Jay and emptied the canister with the venom. With it being the last one, they don't have another chance to get another dose of the venom, and Nadakhan captures Jay, but Nya reveals that Nadakhan emptied the wrong canister, giving the Ninja another chance at stopping Nadakhan. 

Held captive on Misfortune's Keep, Jay is tested as Nadakhan does everything in his power to break the Ninja's will to say his final wish. Meanwhile, Lloyd, Nya, and Cole are stuck on Tiger Widow Island, with no way to get off, so they decided to build a raft to get off. Back on Misfortune's Keep, Jay has dinner with Nadakhan, telling the Lightning Ninja that if a Djinn Prince/Princess marries on Djinn Land, under the Djinn Law the prince/princess will get infinite wishes. Jay tries telling Flintlocke, but Nadakhan thinks he is telling fibs, and the first-mate believes him, so they decided to put Jay in a dangerous game: Scrap 'n' Tap. The winner gets to tap out. Nadakhan kept convincing Jay to 'wish it all away,' but since he's smart, Jay stays in the game, although losing to Monkey Wretch, Doubloon, and Dogshank. After the match, Jay is locked in a hole, having a bruised eye. 

The last remaining Ninja dare to infiltrate the Sky Pirates in an attempt to save Jay and defeat Nadakhan once and for all, using movie magic. Kevin and Dan suggest that the 3 Ninja disguise themselves as Sky Pirates to sneak the poison on Misfortune's Keep, and pass undetected by speaking pirate dialect, apart from Lloyd, who seems to be horrible at talking pirate. They start building a Raid Zeppelin, the blueprint Jay wrote his message on. Once learning pirate talk and disguises as pirates, the Ninja set off to the re-constructing Kingdom of Djinjago realm. Cole climbs onboard, nearly dropping the venom. He secretly walks across the deck, using his disappearing skills. When Cole got to the drinks section, Jay comes out with a vengestone ball and chain, wearing his eyepatch from the Scrap 'n' Tap. Jay asks why Cole's dressed like a pirate but avoids it. 

With only Nya and Jay remaining, they set off to the lighthouse, where they think that Nadakhan won't find the two there. But, when Nadakhan forced Clancee to wish where they were, he finds that he has sailed enough oceans for that to be the Red Kelp of the West Apasso Current. After meeting Echo Zane, the two decide to spruce the place up, having traps set up, weapons, etc., and wait for night. However, Echo spotted the Sky Pirates approaching. During their previous discussion for Jay's last wish, Nya tells him he has to wish for Nadakhan not to be a djinn. A massive fight scene goes on, with most of the Traveller's Tea gone. When they found it in an isolated place, Jay and Nya try to talk it out about who goes to the portal, since it was only big enough for one. Nya tells Jay that she also saw her future: the first time she met Jay. She then continues, saying that Jay has the last wish, and she throws him in the portal. 

When Jay is back in Ninjago City, he starts to gather allies: Captain Soto, Skylor, the Police Commissioner, Ronin, Echo Zane, and Dareth. They make a plan called Operation Land Ho, but when Bucko and Squiffy have heard what they said, they report back to Nadakhan, warning him about Jay and the others. Nya convinces Nadakhan to drop his sword, allowing Jay to grab it and enter the Djinn Blade to rescue Sensei Wu, Misako, and the other Ninja.

When the marriage takes place, Nadakhan has been given the power of infinite wishes. The crew realizes that Nadakhan only wants his power all for himself, so Clancee tells Jay where the Tiger Widow Venom is. Nadakhan banishes Clancee, Doubloon, and Monkey Wretch, but Dogshank and Flintlocke escape and decide to unite with the Ninja against Nadakhan. Jay gives the venom dart to Flintlocke while the Ninja confront Nadakhan and Nya, who has become a reincarnation of Nadakhan's true lover, Dilara. The Ninja attempt to get Nadakhan out in the open so he'll be exposed to Flintlocke's dart, and eventually they succeed in doing so. The dart hits Nadakhan but hits Nya as well. Being the deadliest venom, it kills her, so Jay uses his final wish to wish that no one had found the Teapot of Tyrahn in the first place.