Following the defeat of The Preeminent, Jay and the Ninja face off against the vengeful Djinn Nadakhan. During this experience, Jay discovers some details about his past and tries his best to win back Nya.
Jay is revealed to have told Zane about what he saw in his reflection in the Tomb and is told by him to tell Cole. However, he refuses since they have finally become friends again.
When Clouse was spotted in Stiix, the Ninja went their, disguised, to try and search, only to find no sign of him and while at a bar, discover someone is framing them for crimes they didn't commit. When Misako was arrested, they had to split up, with Jay being the only one objecting.
Jay walks into a bar and tries to get some Ninja Chips, but ends up short-circuiting the vending machine and left before the bartender could recognize him.
Later, he and Cole investigate Mega Monster Amusement Park, but they are spotted by Ronin, who was hired to arrest them. After a fight on the rollercoaster, Ronin turned it off as Jay was still on it, ending up falling into a sack, laid by Ronin and is taken to Kryptarium with the other Ninja.
The Ninja are led by Warden Noble into their cells. Along the way, they met The Mechanic, who wanted Zane for his spare parts. They spent some time in the cell until visiting hours. Dareth told them he sent in a cake with tools they can use to escape, but unfortunately, Cole ate it, along with the tools. When Dareth was unable to further assist the Ninja, he left.
During lunch hours, they were visited by Captain Soto. A fight broke out, and Soto told them he trapped Nadakhan using the venom of a Tiger Widow. The guards stopped them before he could tell them the location of the map to Tiger Widow Island. Instead, he promised to let them know if they could free him.
While the Ninja were stuck in the hole, Lloyd picked his cuff's lock with a plastic fork and broke the others free. Jay was ordered to disable the security cameras. Once they, and Soto, are freed, they were told the map to Tiger Widow Island is in a lantern located in Misfortune's Keep.
In an effort to learn the whereabouts of Nadakhan's pirate ship, Misfortune's Keep, Jay and Nya disguised themselves as police officers and infiltrated the Ninjago City Police Station. During their lunch break, Jay attempted to buy Nya lunch, but realized he was broke, forcing her to cover for him. As they ate, she reaffirmed her stance that they were only friends and that's all they will ever be.
While alone, Jay was confronted by Nadakhan who convinced him into wishing he was never born in a junkyard. He was then instantly visited by the Postman who delivered him a letter that informed him that his father had passed away. In shock, Jay flew his elemental dragon to the junkyard, where Ed and Edna revealed that he was adopted.
Jay went to his real father's home, discovering him to be none other than Cliff Gordon, the actor who played Fritz Donnegan and the author of "Cliff Gordon's Guide to Wooing Women." It was there that he was confronted by Nadakhan who encouraged him to make his second wish. Though Jay was adamant about making another wish, he accidentally let slip that he wished to be left alone, prompting Nya to arrive. In an effort to impress her, Jay used the advice of his father's book and convinced her that the house was his secret hideout.
The two then regrouped with the rest of the Ninja at Yang Tavern where they witnessed via the news Misfortune's Keep attack Ninjago City. Deciding it was their duty to protect the innocent, the Ninja came out of hiding to defend the city. In order to stay together, Jay paired up with Kai but was quickly separated due to an explosive barrel, causing Kai to be whisked away by Nadakhan.
Taking the others to his father's home, Cole immediately confronted Jay on how he acquired the villa as he spent his money on junk food and video games. Jay told him about his encounters with Nadakhan as well as the wishes he made, having him keep it a secret on the grounds that the team won't suffer the same fate as Kai.
After everyone else pinpointed the location of Tiger Widow Island, Jay chartered his father's yacht so as to sail to the island. Along the way, he read his father's guide again to act sensitively to Nya. The team soon got caught in a lightning storm and Jay had to act as a lightning rod.
The team was soon shipwrecked on Tiger Widow Island and discovered Zane had been captured by Nadakhan. Cole, angered by this, outed Jay for making his wishes and forcing him to reveal what he saw in the tomb. Nya then nominated him to get the Tiger Widow venom. All the while, Jay suffered from their antics.
Jay did so, using the guide to get it. However, the Sky Pirates attacked and Nadakhan captured him, leaving the others stranded on the island.
On Misfortune's Keep, Jay, chained to a Vengestone ball, mops the deck while Nadakhan throws water all over the deck to annoy Jay, but still refuses to wish his third wish. Angered, Nadakhan orders him to sweep the bottom of the ship while in midair. Jay is thinking of writing a message to his friends. He fakes a back injury so that Clancee could get Nadakhan and writes the letter on the back of some blueprints, then pretends he is going to escape while being chased by Nadakhan and Nadakhan's Crew. After he successfully sends it, Nadakhan forces him to play Scrap and Tap, a game where Jay has to defeat Nadakhan's Crew, leaving him injured by the Sky Pirates, Clancee offering him an eyepatch which he puts over swollen his left eye.
That night, Flintlocke escorts him to the main cabin to dine with Nadakhan on the Djinn's request. Nadakhan talks about Nya and says when he marries Nya he will have infinite wishes. Jay tries to stop Nadakhan but fails. Jay talks to Flintlocke to go against him saying that Nadakhan will get infinite wishes but Flintlocke does not believe Jay. Ronin and Police Commissioner find Jay's letter and The Ninja, Ronin, and Police Commissioner are off to save him.
Working nonstop on cleaning the Misfortune's Keep, Jay is left drained of all his energy and unable to even stand up. When the Ninja began their assault, Cole found him in Nadakhan's quarters and they made up. Lloyd and Nya were soon captured by the Sky Pirates and Jay and Cole were locked up with the former. They were soon meant to walk the plank until, Cole, Lloyd, and Nya began using their wishes to battle the Sky Pirates despite Jay's constant objections to nobody listening to his. Lloyd soon discovered that Jay's last wish would be what saved everyone and helped him and Nya escape while he and Cole were sucked into the Djinn Blade by Clancee on Nadakhan's orders. Unable to summon his dragon, Nya grabbed him and they were soon able to create an elemental hybrid and escape.
After both Cole and Lloyd are trapped and captured in Nadakhan's Djinn Blade, Nya and Jay are put under protection from the Ninjago City Police Department and sent away to the old lab of Zane's father, Dr. Julien. There, they met Echo Zane and Nya confronts Jay about his feelings towards her. After Nadakhan has discovered where they are hiding, Jay helps Nya and Echo Zane to booby-trap the lab in preparation for his arrival. When the Sky Pirates attack, Jay gets into a fist to fistfight with Doubloon on top of the roof, while Nya fights Dogshank inside the tower.
After Nya sacrificed herself by pushing Jay through the portal opened up by the Traveler's Tea, he lands back in his parents' junkyard, exhausted and injured. After he woke up, he told his parents about everything that's been happening lately with the Sky Pirates, while eating some chicken soup. Jay explains how he believes himself to be in for it against the Sky Pirates and doesn't believe he can stop them and save the Ninja and Nya. In response to this, his dad gets angry with him, explaining that the world's in danger and all he's doing is sitting around sipping chicken soup, laughing it off and tells Jay to scrap together some friends for help. After this, Jay sets off on his journey to stop Nadakhan, waving to his parents and flying off on his dragon.
He then goes off to find various allies, including Ronin, Skylor, Echo Zane, Captain Soto, and Dareth. Once the team has been assembled, Jay briefs them on the whole situation and they begin to detect two nearby Sky Pirates on the roof opposite them. When they're seen, Jay pretends to speak gibberish, while Echo Zane, tries to pinpoint their exact location. After their location is found out, Jay and the others chase after them in the skies of Ninjago.
With Nya dying in his arms, the heartbroken Jay uses his last wish to be that Nya had taken his hand and nobody found the teapot that released Nadakhan. The weakened and overhearing Nadakhan grants the wish, and Jay's wish undoes the recent events that occurred since Nadakhan's release. The Ninja are taken back to the billboard where Nya takes Jay's hand and they kiss, while Clouse is spotted by the Stiix citizens and chased away before he could even release Nadakhan.