Following the defeat of The Overlord and Zane's sacrifice, the Ninja went their separate ways with Jay now being the host of television show. When tracks him down, Jay refuses to rejoin the team due to Cole and his role in straining his relationship with Nya but goes along with Lloyd. When Lloyd gathered the other ninja, the latter tells them he wants to find a replacement for Zane which the others disapprove before they fight some thugs and learn that Zane is still alive.
After Zane's sacrifice, the team broke up. Jay now hosts his own T.V. show to find a new hero for Ninjago. He introduces the player as Cathy, a returning contestant and asks why she came back after losing last time she competes. She states that a Ninja never quit and starts jumping through obstacles. However, she fails but is proud to have gotten farther than the previous time. After the game is over, Jay goes to his dressing room, where Lloyd surprises him and tells him to rejoin the team. Jay declines, due to his hatred against Cole for Nya's feelings towards him and Lloyd disappears, while telling him to visit him if he changes his mind. He later reunites with Kai, Cole, and Lloyd. Lloyd informs the Ninja his new plan: hiring a new Ninja. The others completely dislike the idea, saying Zane is not replaceable. They quickly get interrupted by Eyezor and his gang.
The Ninja go to the back of the shop where they lose sight of Eyezor's gang but see a drawn picture of Zane attached to a shrine with an invitation to a Tournament of Elements. They discover from the invitation that Zane is still alive and to find him they must enter the tournament to do so. With other options, they decide to accept and are walking onto the ship when Garmadon comes and tries to stop them, warning them that Master Chen, who invited them, is a dangerous man. Lloyd retorts by saying that they have to find Zane. Against the better judgment of Clouse, Chen's second-in-command, Garmadon accompanies the Ninja on board, where they meet the other Elemental Masters.
The Ninja learn from Garmadon that the fighters on board are descended from the original Elemental Masters.
The ninja are guided to their rooms with Jay being amazed by the technology inside. Soon, he takes a bath when Bolobo enters his room, trying to find a Jadeblade. The Blue Ninja puts on a towel and knocks him to the floor, only to find a Jadeblade in a light. Bolobo takes it, prompting Jay to turn on Starfarer which amuses the Master of Nature, allowing Jay to whack him with his towel, while commenting on his room.
The ninja all win a jadeblade as they watch as Karlof who lost his fight with Kai is eliminated from the tournament.
Later at lunch, the ninja converse about investigating the island before Jay rudely turns away Paleman for attempting to join their table. After this treatment was pointed out to him by Cole, Jay remarked the island is getting to him and tells them he'll see them tonight.
Later that night, everyone arrives, but as Jay comes by, Skylor comes out of her room, forcing Kai to push the Master of Lightning off his balcony. After the Orange Ninja returns into her quarters, Kai helps Jay up and into the Master of Fire's room, describing the difficulty of sneaking out. When Cole discovers a hidden room under the Master of Fire’s bed. The Ninja enter the tunnels where they find two holes peeping into Skylor's room, which Jay looks through first. While watching Skylor train for a few moments, Jay and Kai see Skylor pull out a flame on her hand, which would mean that she is also a holder of fire, like Kai. After telling Lloyd and Cole, Lloyd points out that, if the current elemental holders are related to the original ancestors, it would've also meant that Skylor and Kai was related.
This is soon brushed aside, as they continue making their way through the tunnel. After travelling further into the tunnel, they come across a squad of cultists who they subdue and take their clothes.
Disguising themselves as cultists, they infiltrate the ceremony of the Anacondrai Cultists, as they see Chen's plan unfold when he steals Karlof's element. Startled by this display, the ninja realize what Chen's plan is, as Cole noted that Chen used Ice, which meant he already stole Zane's power. As they talk amongst themselves, their chocolate tattoo melts and the cultists realize that they are "impostors," Chen signals his warriors to kidnap the intruders forcing them to flee. The Ninja lose the cultists, but are trailed by a large Anacondrai Serpent. They barely make it out, and promise to stay within the rules until Zane is found.
Unknown to the ninja in the hidden room, Clouse held up a piece of cloth from Jay's gi that got caught in the mouth of his serpent, revealing the fact he knows the Ninja spied in the plans of Chen.
Despite seeing the truth of the Tournament, he decided to enjoy his next day off, which disgusted Cole and getting them into another argument. Although he states none of the Ninja are competing for the day, Chen immediately announces Kai as one of the competing masters. After the Ninja of Fire defeats Ash, the Ninja and Garmadon cheer for him. Later, Clouse arranges for Jay and Cole to fight each other later that evening to which Kai suggests enlisting Neuro for aid. After they succeed in turning Neuro to their side, they attempt to get him to find a way to stop the fight but this fails. The battle begins where neither Ninja hold back expressing their pent up aggression towards one another until Cole states he doesn't want Jay eliminated and that Chen is their enemy.
Upon hearing this, the blue ninja admits what happened between him and Nya was his fault and agrees to fight without using their powers. To this end, Chen decides for the both of them to be eliminated. Jay tells Cole to take the Jadeblade as he considers himself lucky to still be in the tournament, but Cole throws it to Jay, telling him to win for him, that he should have let him have Nya and that he should have backed out before being eliminated, renewing their friendship and ending their rivalry.
Jay watches Skylor fight Jacob Pevsner with Lloyd and Garmadon just before Kai arrives though steps on the fighter's feet in the process. Jay is concerned that the other competitors will gun for them so long as they're a team, though Lloyd says they are a team, even with Cole and Zane missing.
Jay fills Garmadon in on his crush on her until they found out they might be related. Garmadon explains that Skylor's element isn't Fire—it's Amber, meaning she can absorb another element, which immediately brings Kai's feelings back. Jacob soon has the advantage using blow darts, though Skylor tricks him into firing into paper, where the sound of the air throws him off long enough for her to break the last vase and take the Jadeblade. After Jacob is eliminated, Chen announces he initially wanted to give everyone jewels for their work in the Tournament, but, due to Jay's fight with Cole yesterday, he rejects the idea and takes away everyone's private suites, forcing them to sleep in the chow house. As Jay and Kai berate each other while the other competitors leave, Garmadon warns them that if they don't make friends with the others, they'll try to eliminate them by any means necessary.
While the competitors rest, the remaining three Ninja discuss a plan, but quickly jump back to their beds just as Clouse arrives. He orders Master Chen’s servants to add roller-skates to everyone’s feet, making the contestants curious, while Jay is excited to skate, stating that he's skating champion.
Before the event, the ninja realized Garmadon was right in considering the way they treated their opponents as a majority of the contestants joined Chamille's team in the Thunderblade race, resulting in them being outnumbered. During the race, Jay decides to make an opening by electrocuting Neuro, which works until Kai bumps into Lloyd.
As the race goes on, Chamille is still ahead of Lloyd by one point, Jay then whips Lloyd only to discover it's Chamille in disguise. Jay tries to help Lloyd once Chamille has him ambushed and succeed in making him drop his Jadeblade. When Paleman then takes it, Jay manages to take it back and knocks him off the track. Everyone does whatever they can to stop the Ninja (with only Kai taking the hits), with Chen even releasing a buggy to extend Chamille's lead.
Lloyd is soon ambushed by Paleman, Shade and even Neuro, and when Jay tries to help, Turner accelerates him around the track and into the Green Ninja, though it helps his back. Skylor comes up to Kai, saying he's convincing and Lloyd will soon be eliminated.
With the score now 8-5, Kai decides to help, despite not keeping balanced, and uses his powers to hit Chamille and making her drop her Blade, allowing Jay to take it. Jay approaches Kai after he is brushed off by Skylor and informs him of Lloyd's progress, though Kai now realizes Garmadon was right about distrusting the others. He then states if everyone knew about Chen's true intentions, they'd help: Chamille then takes back her Jadeblade.
After Kai decides to reveal the real nature of the Tournament to Skylor: upon mentioning the spell, which causes Paleman becomes interested. Jay and Lloyd do the same to Turner, who doubts it but Neuro confirms it after he stops Tox from attacking them. Jay is surprised the Master of Mind had chosen that moment to help, to which he explains he wanted to be on the winning team. Chamille attacks Kai and he lands near the buggy, allowing him and Skylor to take it. They drive up to Lloyd and let him take it, where it transforms into his color. While the others keep Shade and Tox from attacking the Green Ninja, Chen goes all out on his traps, all of which fail. The score becomes tied and Lloyd tries to convince Chamille to join them, though she pulls him out of the buggy, leaving them to go head on in a sword fight.
Chen becomes worried of Lloyd winning and orders Clouse to use his Magic, but he's stopped by Garmadon. The scorekeeper then tries to rig Lloyd's score, but Skylor, having obtained Gravis' Gravity, has him float helplessly. The two racers soon cross the finish line just as time runs out, with the final score being 13 each. However, Chamille is revealed to have dropped her Jadeblade, making Lloyd the winner.
Skylor then drops the score keeper, jokingly changing Lloyd's score to 106, and having Garmadon remark that his son broke Chen's record. Chen, however refuses to have the event count, claiming Lloyd cheated and is disqualified, though Turner stands up for the Green Ninja and states Chen cheated, where the Master claims what his rules says, goes. Paleman, Kai, and Jay protest if Lloyd's out, then so are they whereas Skylor states if everyone is eliminated, there is no Tournament. With that along with Clouse confirming it, Chen is forced to comply and eliminates Chamille. As everyone cheers for Lloyd, Skylor warns Kai that because of this, Chen will do anything to eliminate the Ninja. Kai then states that as long as everyone sticks together, there's always hope.
With alliance on their side, the Ninja are confident things are going their way until Chen announces to all that he will give the winner his staff which causes the alliance to break up. Jay is soon pestered by a Kabuki and it's revealed to be Nya in disguise, who is proud that Cole and Jay renewed their friendship before telling them that a spy was hidden among them which how Chen knew of their alliance. The Ninja then have Nya search for the spell Clouse intends to use. Things looking better; the Ninja receive a fortune cookie from Skylor which tells them that Cole and Zane will be breaking out. Relieved that Cole found their friend, they decide to search for their mysterious spy.
For the next event in the tournament, Jay (his leg now in a cast) and the other fighters boarded a blimp and were taken high above the island. There, he and Griffin Turner argued over who would be eliminated first in the tournament. Before long he and the others were dropped out of the blimp by Chen with the promise of being advanced to the final round if he were to find Nya first. Jay was successful in grabbing one of the parachutes and deployed it, though he landed in a tree on the island. Shortly after arriving, Chen announced through the loudspeakers that he had left items throughout the island to help in the search. Jay muttered to himself the he would never trust a treat from Chen, but soon stumbled on a mech. Tired of walking due to his broken leg, Jay decided to take his chances and use the mech.
This decision would eventually prove consequential as Jay soon encountered Clouse who informed the master of lightning that his time in the tournament had come to an end. Though Jay manged to fight off the sorcerers' initial attacks, Clouse soon created a mech of his own and they squared off. During the mech fight, Nya arrived on the scene and tried to tell Jay what the spell was. However due to Clouses continued attacks, Jay ordered her to find the others just before Clouse damaged the mech enough to trigger an explosion which Jay nervously laughed at as they were captured in it. Despite this, Jay was shown unharmed but was captured by Clouse thrown in the cage with the other captured elemental masters. Jay then watched as Chen threw a recently captured Kai in the cage before telling his friend that Lloyd would come to save them something an overhearing Chen stated he was hoping for.
After his capture, he and the other captured Elemental Masters were put in Vengestone shackles as they were brought before Chen. Despite being led to have his power taken away with the others, Jay decided to rely on positive thinking and believed Lloyd would swoop in and save them at the last second. When he stated this belief to Chen, he waited for this to happen but got bored and took the masters' powers, much to Jay's disbelief. He was then taken to the factory with everyone except Kai, who was released on Skylor's wishes.
After being told to get to work, the Master of Lightning soon reunited with Cole and Zane, telling the latter he looked amazing in his new form. After being informed of the construction of the Roto Jet, Jay broke from his positive belief and questioned the construction of the jet being underground, something Cole agreed with. The Master of Earth then asked him about Kai's current whereabouts, to which he replied the Master of Fire was getting special treatment.
Later, Jay is contributing to the completion of the Roto Jet when Zugu discovers the ruse and Cole begins an assault on the cultists while everyone else pushed the jet. They save Nya and Garmadon from Clouse's Serpent and soon burst into the ceremony room, narrowly saving Lloyd and Skylor from the corrupted Kai. The ninja and the Elemental Masters fend off the cultists until Kai destroys the crystal of the Staff of Elements, effectively restoring everyone's elemental powers and over power the cultists.
Reunited, the Ninja use Spinjitzu capturing the remainder of the Cultists, except for Chen, Clouse and their top men, who captured Skylor. The Elemental Masters seize control of the island, in the midst of celebrating, Jay laughs with the other Masters when Zane plays his humor switch.
Jay had the other fighters sink the ferry so Chen and his forces would have no means of escaping the island. He met up with his friends where they assured Kai they will find Skylor. Jay and the others are told by Griffin Turner that Chen had found a way to complete his spell by using Skylor's powers as the way. The Ninja go off to pursue Chen and save Skylor but Zane gets separated from them much to Jay's worry but the latter tells him to go off without him.
When Chen's army transform into Anacondrai, Jay and the others battle them but are overwhelmed and forced to retreat. Jay then sees Garmadon transformed into Anacondrai and attempts to attack him only for Lloyd to stop him and explain what happen as Jay lists all the forms Garmadon took and tells Garmadon to pick a body and sticking it with it.
When Chen's army manage to escape, Jay ironically complains about having no way to follow them before seeing that Zane had manage to summon a Titanium Dragon being amazed by it and asking Zane how he did it as the latter told he faced his fear. He soon witnesses Kai and Skylor arrive on an Elemental Fire Dragon, supporting Zane's words. Encouraged by his friends, Jay summons an Elemental Lightning Dragon and he and the others chase after Chen's army on their Dragons.
Flying back to Ninjago on his Dragon, Jay carries Nya to the city and explains to Kai that mastering the ability to summon a dragon took time. They arrive in Ninjago only to find Chen hasn't attack before deciding to head for the Samurai X Cave while having their allies watch over the city. Once at the cave, they reunite with Wu and Misako before deducing Chen's next move and after Jay points they know so little about the Anacondrai they decide to go to Kryptarium Prison and visit Pythor. Though he at first refuses to help them, he is persuaded after seeing Garmadon as an Anacondrai. The prison is soon attacked by the Anacondrai Cultists, Jay, Kai and Cole go off to fight them as the others stay behind with Pythor.
As Cole complained about the cultists having weapons, Jay remarked everything was a weapon in prison which he showed by using a toothbrush against a cultist. Zane joined the fight as Jay told Wu and the others(who realized Chen's goals) to run after the prison was put on lockdown however, the inmates got loose beginning all-out brawl. Jay remarked since they already fought most of the prisoners they should leave which his friends agree with. Cole then uses his strength to break through the walls as Jay complains that when people talk about breaking out they do so "quietly" not literally as the prisoners pursue them. The ninja make it to the courtyard as the Anacondrai Cultists make off with Pythor, Wu forbids Cole from breaking the walls as they couldn't let the prisoners escape. In response, Zane creates an ice trail which the ninja use to escape as Kai uses fire to destroy it preventing the prisoners from following them allowing the Warden and guards to arrest them.
The ninja returned to the Samurai X cave where Nya explains that Chen shipped twenty noodle trucks which they speculate can hold several Anacondrai. The ninja contact their allies for aid but to their surprise the trucks separate which Jay questions on they should be heading for the city. Misako states there were many villages in the directions the trucks went off to as Lloyd makes the decision to have everyone split up to defend the villages. Jay complains at first since they just got back but Garmadon tells him they if they don't act Ninjago will be in danger something Jay realizes and moves out with his friends.
Using his dragon, Jay pursues a noodle truck determined to not allow it to reach a village. After forcing the truck to make a halt in an icy region, Jay subdues the driver by tying him up before he prepares to deal with the Anacondrai. However, upon opening it he discovers it is empty and sadly realizes that Chen deceived them in his goal of separating the elemental masters. Like many others, he lost his dragon out of fear while Chen and his army invaded villages without problems.
Having realized Chen's plan and being stranded, Jay is contacted by Nya of Chen's actions but can't understand it due to the bad reception (caused by Chen taking over the airwaves). He soon decides to take the noodle truck back to the cave after getting mental message from Lloyd through Neuro.
Once at the cave, he regroups with his allies where she informs them that Chen has taken over the entire eastern coast. Wu points out that the Corridor of Elders will be the best place to make their final stand, and the elemental masters agree. The Ninja journey all over Ninjago to rally support from the citizens, with Jay going to the junkyard to get his parents and the aid of others.
The Ninja, elemental masters, citizens, and Serpentine get to the Corridor and start the ultimate battle against Anacondrai. Pythor escapes Chen's camp riding a rat and carrying Chen's spell book. He gets to the battle and tells Lloyd to take him to his father because he knows the way to end the battle. Later, Lloyd opens the portal to the cursed realm and unleashes spirits of Arcturus and his troops who quickly curse Chen and his soldiers turning them into ghosts. They all get sucked into the portal, which then explodes after closing off, ending the war.
The ninja and the elemental masters then celebrate their victory, with Jay and Kai being hugged by Karlof as they all promise to offer in the future as they part ways.
On the top of the corridor, the ninja, Wu, Misako, and Dareth sit around a fire on a broken statue, watching construction workers building statue of Garmadon in the corridor. Lloyd tells that today they will say goodbye to a legend and burns the book in the fire.