After Zane's sacrifice, the team had split up, with Kai going off to wrestle in an underground fighting tournament, becoming known as the "Red Shogun." One day, Kai is visited and is persuaded by Lloyd to rejoin the Ninja, although he is reluctant due to not standing out like Lloyd and Zane, but goes to meet with the Green Ninja. Kai sees Lloyd invited Cole and Jay as well, and Lloyd tries to get them be a team again, even suggesting replacing Zane; but they all refuse, even stating maybe without Zane, there was no team. The Ninja soon fight a group of thugs but when the thugs retreat, the Ninja find a poster stating Zane was still alive and receive an invitation from Master Chen to enter a Tournament if they wanted to find him.
The Ninja then set out to find him being joined by Garmadon and while on board the ferry, they find there were others with abilities like them, one particular master catching Kai's eye. During their time on the island, the Ninja secretly conduct the search for Zane, and discover that Chen is really using the tournament as a way to mask his intentions of stealing the masters Powers.
Following Zane's sacrifice, the team has split with going to wrestle in an underground Slither Pit known as the "Red Shogun." After a fight, he rests to drink some juice, when Lloyd arrives and asks Kai to return to the team. Kai refuses the offer, saying Lloyd doesn't need a team, and wishing it was him who gave his life instead of Zane. Lloyd reminds him he always wants to be the one, using his obsession of becoming the Green Ninja as an example before telling him to think about someone other than himself. Lloyd goes away telling Kai to meet him at a noodle shop as Kai ponders on it.
Very soon, Kai goes to the park to see the statue of Zane as the Titanium Ninja, causing him to reflect on his time with late friend as he sees the Falcon appear. Kai then decides to take up Lloyd's offer and goes to see him. However, Kai wasn't the only one to meet the Green Ninja at Chen's Noodle House: Jay and Cole had also been convinced and has met Lloyd there too. Lloyd informs the Ninja his new plan: hiring a new Ninja. The others completely dislike the idea, saying Zane was not replaceable and Kai states maybe without Zane there was no team. They quickly get interrupted by Eyezor and his gang who attempt to rob the store. However, the Ninja intervene quickly defeating the thugs who run away.
The Ninja pursue them and go to the back of the shop but see no sign of the thugs instead a drawn picture of Zane attached to a shrine with a note stating that he was still alive as well invitation to a Tournament of Elements.
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.
While on board, Kai and his friends see other people who received invitations and saw they had powers. Kai asked Garmadon why he or Wu never told him there were others with abilities like them as Garmadon explained there were some things they didn't want them to know. He then reveals everyone on board was descended from an Elemental Masters listing a few examples of the others on board. Kai then notes the same went for his sister but states she can't do what he can as Garmadon tells him its possible Nya can as she only needs the power to be awoken to do so.
Kai begins to take an interest in a cloaked woman and questions Garmadon on what her element is, but he didn't know as he'd never seen her before. Soon enough, Kai sees Karlof, the Master of Metal trying to take the woman's cloak and starts to insult him until the two begin fighting all over the ship. Just as Karlof pinned Kai and was about to finish the fight, Clouse calls it off: the woman helps Kai to his feet and copies his powers without him noticing. Clouse announces that they reach Chen's Island, and while the Ninja wonder where they will find Zane.
The contestants of the Tournament of Elements finally reach Chen's Island, rushing to be the first to see and go into Chen's place. The boat sets dock, allowing the people to escape the ship. The Ninja group together, while Kai loses conscious staring at . Kai immediately blocks the Ninja's path, telling them that "Girls go first." The heroes of Ninjago reach the underground fortress located in the island. Clouse arrives, commanding the contestants to welcome Master Chen. Master Chen brings his servants to welcome each contestant to their room. The Master of Fire enters his room first. His earliest discovery was his Kai poster. He wanders into his patio curiously, and glances at a familiar figure, who is also his neighbor: a Ninja girl clad in an orange Ninja gi. Kai attempts to introduce himself and use his Elemental power to win her over, but the girl—Skylor, by name—throws him off by flirting back, making him quickly lose control of the fireball in his hand. His reaction to the burning seems to amuse her.
Master Chen announces the competition starts now. Kai and Skylor see a Jadeblade on top of their roof. Skylor preforms back flips to get to the location of the blade. Kai jumps up too, and accidentally knocks her down. He managed to grab her leg, stopping her from falling. He flings her up; however, she reaches the blade, now making only one Jadeblade left and Karlof heads to the last one. Kai realizes and follows Karlof. Kai's archenemy won the battle, but before Karlof could hand it in, Kai unscrewed his Metal fist, getting a chance to win. Kai flies to Chen's location putting the blade in its spot to win.
Since Karlof has lost the contest, he is sent to Chen's secret location in the dungeon. Kai suggests they have a meeting later in his room. The Ninja had entered Kai's room with the exception of Jay since Skylor has arrived, therefore making the Red Ninja push Jay. After Skylor had re-entered her room, Kai helps Jay get up, apologizing for the mishap. The Ninja discuss the tournament while Cole lays down on Kai's bed, accidentally triggering a button again which reveals a secret entrance. Cole informs his friends, and they silently travel to the secret room. In the secret cave, Kai, Jay, Lloyd, and Cole hear Skylor shout in her room. They observe her room with little peeking holes, and surprisingly find her using the Fire element, which causes Cole tease the Red Ninja by singing that "Kai's heart is on fire." Soon, the Ninja face Chen's minions, but silently hide behind a rock while defeating the four minions. After they defeat the minions, they take their outfits to blend in and look like Anacondrai Cultists, and go to Chen.
Master Chen then has his followers bring out a captured Karlof, and the Ninja are horrified to witness him steal Karlof's power with his Staff. The Ninjas' soon note that Chen used Ice when he cast the spell, which meant he already stole Zane's power too. As the Ninja realize Chen's goal is to steal everyone's power, their identities are revealed and Lloyd commands the Ninja to run out of the place. While running, Cole trips on a booby trap which sets out traps and a huge snake (which Kai notes is the second biggest snake he's seen).
Running away from the giants snake, they finally make it back into Kai's room. They now promise to stay within the rules until they find Zane.
At Chen's island, the Tournament of Elements is on break. All the competitors are in the cafeteria eating lunch. The Ninja are still shaken up from Chen stealing Karlof's powers and try to come up with a new plan to find Zane. Chen then announces the six masters competing to get the jade blade next. The masters consist of Griffin Turner, Gravis, Ash, Bolobo, Neuro, and Kai.
The match between Kai and Ash takes place on a bridge over a volcano, with the jadeblade and the competitors on a wooden bridge. Kai goes straight for the blade, but Ash flips the bridge over, causing it to fall on a rock below. Kai climbs under the bridge and attempts to kick Ash, but the master of smoke uses his powers to evade the attack. Kai continuously attacks Ash, with none of his blow landing while Ash keeps disappearing and reappearing and his punches landing, eventually sending the master of fire through the bridge and hanging. Kai initially struggles to hang on to the plank worrying Skylor, but he flips himself back onto secured planks and uses his Spinjitzu to push Ash back though the end result is the same. Lloyd encourages him to use his powers, so Kai then launches multiple fireballs, only for Ash to dodge them while they begin burning through the bridge. As Kai and Ash's battle continues, Clouse attempts to use his Magic though Chen prevents him from doing so, enjoying the fight. Ash manages to apprehend Kai, but he launches one more fireball which successfully burns through the last of the bridge, sending both of them onto the rocks below. The two then battle in midair over the Jadeblade where they're evenly matched until Ash makes for the blade. Kai then attacks him, where he uses his powers to avoid being hit: Kai uses this to take the blade and end the match with Ash eliminated.
Soon, most of the contestants are looking at the brackets and when the Ninja see for themselves, they're shocked to find Cole and Jay have been set up to fight next. The Ninja confront Clouse about this, but he brushes it off. Kai suggests they ask Neuro for help, but he denies as helping them might hurt his chances in the tournament. Lloyd manages to convince him by letting him read his mind and seeing what happened to Karlof. Later Neuro tells Kai what he discovered: Clouse has a spell book where the page marked 149 has a spell that requires everyone's powers, though he couldn't find a way to stop the fight.
During the battle Jay tells Cole to take the Jadeblade as he himself is lucky to still be in the tournament, which he does, but throws it to Jay like a true friend, saying he should have backed down with Nya before telling the Blue Ninja to win it all. Cole loses, though Garmadon tells Kai, Lloyd and Neuro that he did the right thing.
Kai is seen running around outside the temples, appearing to be lost. He then runs inside one upon hearing Chen's voice announcing the next fight. Inside, Skylor is about to fight Jacob, the Master of Sound and they begin to smash vases in order to find a Jadeblade. Kai soon arrives and makes his way to his seat, stepping on everyone's toes in the process, soon realizes Skylor's fighting just as she sets Jacob's sitar on fire, while 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 other elements with a single touch, which immediately brings Kai's feelings back. After Jacob is eliminated, Chen announces he initially wanted to give everyone jewels for their work in the Tournament, though due to Jay's fight with Cole yesterday, he rejects the idea and takes away everyone's rooms, forcing them to sleep in the dining hall. 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. Clouse only says Lloyd will fight Chamille, Master of Form before leaving. Lloyd is confused as to who Chamille is, to which Kai seemingly explains how she can disguise herself to find another's weaknesses. Lloyd points out his only weakness is his aching back, but as Kai skates away, he appears on the other side, struggling to balance on his skates. Lloyd soon realizes that Chamille, disguised as Kai, tricked him into pointing out his only weakness to her.
During the Thunderblade Race, Skylor asks Kai what's left from stopping him from winning the tournament if Lloyd was out, to which he says he doesn't think of it before she knocks him down. By now, Lloyd and Chamille have each gained a point and have caught up to the others, who stop Lloyd from passing. Jay decides to make an opening by shocking Neuro, which works and stops everyone else: however, the plan fails as Kai accidentally knocks into Lloyd, causing him to fall behind by one point. Chamille orders Shadow to hit Lloyd's back, succeeding and making him drop his Jadeblade. Paleman then takes it, only for Jay to take it back and knock 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. Skylor comes up to Kai, saying he's convincing and Lloyd will soon be eliminated.
With the score now 8 to 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. Skylor attempts to berate Kai for what he did, though he snaps and says that as Ninja they stick together, causing Skylor to regret trusting him. Jay approaches him and informs him of Lloyd's progress though Kai now realizes Garmadon was right about not trusting the others. He then states if everyone knew about Chen's true intentions, they'd help: Chamille then takes back her Jadeblade. Kai latches onto Skylor, explaining what he meant and revealing the real nature of the tournament: upon mentioning the spell, Paleman, Shade, and Griffin become interested, and are convinced upon Neuro's testimony. 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. After Lloyd wins, Chen refuses to have the event count, claiming Lloyd cheated and is disqualified, though Griffin stands up for the Green Ninja and states Chen is the one who 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.
As it turns out, the banquet is being held for the eight remaining competitors who have made it to the second round. Chen tells the remaining eight that he knows that they have a secret alliance and that that the tournament is about stealing everyone's powers. To crumble the alliance, Chen lies and tells that whoever wins gets his Staff of Elements. Nya goes to the banquet and tells the Ninja that she's undercover and that one person in their group is a spy. This leaves the Ninja curious before Skylor arrives with a fortune cookie that says Cole and Zane will be breaking out, which elates the Ninja that Cole found their lost friend.
Later in Kai's quarter, all the fighters try to determine who the spy is. Garmadon suggests checking their backs and the one who has a snake tattoo on their back is a spy. Eventually, it comes down to Shadow and Skylor, the latter attempting to get Kai on her side by saying he didn't trust her: he stated he did and wanted the others to trust her, too. Before she did, Shadow made his escape declaring he wasn't the spy or the ninja's friend, so the Ninja and the remaining masters assume Shadow is the spy. Kai tries to apologize to Skylor, but she refuses to listen and shows him and the Ninja her back without a tattoo, leaving him guilt-ridden. Unbeknownst to them, Skylor truly was the spy and had hidden her tattoo using the power of Form.
For the next round of the tournament, Kai and the other remaining fighters boarded a blimp and were taken high above Chen's Island: while on the blimp, Kai argued with Shadow as everyone still considered him the spy. Once they were high above the island, Chen revealed to Kai's horror the objective of the next round was to capture Nya, who had proof of Chen's plan. The masters were then dropped out of the blimp along with parachutes and Kai was successful in claiming one, though landed close of the island's volcano.
While searching for Nya, Kai noticed a rustling in the bushes and ignited his hand with a fireball only for it to be Skylor. The Master of Fire asked if she would help him in his search and the two set off together. However they had not gone far when they noticed a massive fireball across a pond. Kai began hoping from log to log to get across, but Skylor froze the pond to get there quicker, causing Kai to realize she saw Zane and that she was the spy, having used Chamille's power to hide her tattoo. To his even greater surprise, she revealed that Chen was her father, who using the power of smoke, appeared beside them.
Chen declared that Kai's time in the tournament was over and ordered Skylor to seize him, though Kai used his fire Spinjitzu to get to land. There however, Chen used his staff of elements to trap the master of fire in vines, capturing him. Kai was taken to the D.B. Express and thrown in the vengestone prison along with the other elemental fighters. He was told by Jay that Lloyd would come for them as they were taunted by Chen who wanted Lloyd to come try. As Chen laughed, Kai stared at Skylor heartbroken by her betrayal.
In the Anacondrai Temple, Kai, Jay, Griffin Turner, Neuro, Paleman, and Shade are led in chains made of Vengestone to have their powers taken away. As most of the master's lament on not heeding the ninja's warning, Jay tries to maintain positive attitude which Kai berates him for given the situation.
Upon being brought before Clouse and Skylor, Kai questions how she could help her father knowing he'll need her element for the spell as well. Saying she had no choice, Kai asks who planned to have him fall for her, which shocks Skylor. Chen raises his staff and takes the master's powers. Upon Chen ordering for the masters to be sent to the factory, Skylor begs for Kai to be spared saying he can help them which he complies with.
Chen shows the Red Ninja his trophy collection (containing parts of the Ninjas' past adventures), though Kai responds that without the staff, he'd strike the villain down. Chen noted even without his power the fire still burns in Kai before he explains that unlike Kai and Skylor, who got her powers from her mother, he himself had no abilities and was told he'd amount to nothing. He then shows Kai a portrait of Arcturus and announces with Lloyd's power, he'd be unstoppable since he will turn his followers into Anacondrai. When Kai asks why Chen was telling him this, he tells Kai he knows he's still jealous Lloyd became the Green Ninja and offers to give him the power he wanted to try for so long. However, Kai refuses to betray his friends: Chen counters this by promising dark secrets about his parents his masters never told him which surprises Kai. Before he can inquire about this, Clouse comes to tell him of Lloyd initiating his plan soon and they leave Kai to consider his offer.
After Lloyd sneaks into Chen's Palace and falls into another one of Chen's trapdoor into a cave made by Clouse's serpent which pursues him. Kai appears and gets the Green Ninja out and advises him of the situation and plan, but Lloyd refuses and says he needs to face Chen. With that, Kai apologizes to Lloyd blowing out his torch and leaves while Lloyd finds himself with Chen in the throne room. Shocked that Chen managed to turn Kai against him, Lloyd proceeds to battle while trying to talk some sense into Chen. However, the man uses everyone's elements to overwhelm the green Ninja and defeats him.
Nya wakes up in the dungeon of the snake where, along with Garmadon, she's chained to a post. Chen, Clouse and Skylor approach and inform them of Lloyd's defeat and that his power will be taken soon. Nya questions how they were able to defeat him to which Kai enters, saying Lloyd never stood a chance alone. Garmadon, now enraged of Chen turning the Ninja against each other like he did to their ancestors, grabs Skylor and threatens her unless he and Nya are released: they call his bluff due to his reform and he's forced to release the Orange Ninja, shocked with her father.
Clouse opens a tunnel door for his snake to enter after its nap while Nya tries to talk sense into her brother as Kai tells her this was it was to be but winks at them, revealing he only pretended to switch sides to gain Chen's trust relieving them. As Chen and Clouse leave to prepare for the ceremony, Kai pulls Skylor back and explains he can get the staff. Skylor asks why he'd tell her after her betrayal: Kai states she let him go for a reason, with her feeling for him being the most obvious choice which she admits.
In the ceremony Lloyd questions why Kai would betray him, though he tells him not to worry but keeps up his act. Chen then has Skylor give up her powers. By now, Skylor has completely lost her power and Chen proceeds to take Lloyd's Energy. As Clouse begins the spell, Kai tells Chen he forgot one more element: the "element of surprise." Skylor then kicks the Staff of Elements out of her father's hands and Kai uses it to free Lloyd, who realizes Kai's plan. With the staff, Kai holds off the Cultists and manages to freeze Clouse. Lloyd tells him to destroy the staff, but Kai begins to become corrupted by its power. Just before he uses it on Lloyd and Skylor, all the escaped elemental masters burst in (among them being Jay, Cole and Zane) causing him to drop it. Regaining his senses, Kai spots the staff and runs to it quickly grabbing the staff before Chen does and destroys it, restoring everyone's elements allowing them to overpower the Cultists.
With the Ninja reunited as a whole once more, they do Spinjitzu and defeat the remaining Cultists before Chen, Clouse, Eyezor, Kapau, Chope, and Zugu escape with Skylor as their prisoner.
With Chen in hiding, the Elemental Masters capture the remaining Cultists and seize control of the island. Nya and Garmadon assure Kai they'll find Skylor while Kai expresses surprise at finding an old friend and making new ones, including a new kind of friend in Skylor. Garmadon once more assures they'll find her, with the battle now over for the time being, Kai and the others laugh at one of Zane's new modifications.
On Chen's Island, the masters make sure that Chen and his forces can't escape by destroying any means off the island. As they do so, the Ninja search the palace but find no sign of Chen as Lloyd comforts Kai about Skylor, saying that while she couldn't pick her family, she picked a good friend, with the addition of Cole saying with no other way off the island, they'll find them. Garmadon congratulates the five on bringing the Elemental Masters together and sticking together, though he warns them to keep their guard up. Later, Griffin Turner and Neuro inform the Ninja, Nya, and Garmadon that Chen plans to use Skylor's absorbed powers to finish the spell and turn the cultists into Anacondrai.
After getting Skylor's location, Kai takes off on one of the crushers while Jay takes the mech, Garmadon and Cole take the Jet, Zane takes a buggy, Nya takes the DB Express and Lloyd leaves on his dragon. Later Skylor is now being chased by Eyezor and is saved by Kai, who crashes his chopper into the thug's own bike. Kai takes a rocketboard for himself and the chase begins again when Chen starts to pursue them in the bladecopter. Combining their Fire, they create a smokescreen which Chen flies through, sees Kai, and notices Skylor disappeared not seeing she used her Form to disguise herself.
Kai emerges from one of the buildings, having alerted the team and takes an interest in exploring the town, but brushes it off to bring Skylor back. However, the two are ambushed by Kapau and Chope and captured in an Element-blocking net. Later in the crystal caves, the transformation is revealed to have begun, Kapau reciting the spell in Clouse's place. As Chope finishes the spell (Kapau having fainted from its effects), Kai urges Skylor to resist the transformation. However, the transformation is completed which Chen cheers for while. Kai attacks Kapau, Chope, and Chen though none of them are affected due to their thick Anacondrai skin allowing Chen to knock Kai away but Skylor breaks free and attacks her father before he can finish Kai.
Accepting her new form, the red Ninja leads her two out of the cave and return to the coast riding Kai's Elemental Fire Dragon supporting Zane's (who summoned a dragon as well) theory of conquering their fear, convincing and encouraging everyone to unlock their dragons. With dragons, they begin flying after Chen as Kai states that although Chen brought them there so only one of them would remain, he didn't think that together, they were one.
On Dragons, the Elemental Masters fly to Ninjago in order to stop Chen and his army. They arrive a day after Chen; Kai wondered how they lost time as the others bring up they had to retrieve those who are not Elemental Masters and how hard it took for them to master summoning dragons. Once in Ninjago, they find Chen hasn't attack yet and when people run after seeing Skylor as an Anacondrai, Kai consoles her by telling her she's with them after she wishes says could still change.
To avoid causing a panic with Garmadon and Skylor, they take them back to the Samurai X Cave where they reunite with Wu and Misako to deduce Chen's next move. The Ninja visit Kryptarium Prison, where they speak to Pythor of how to combat them, though he is initially against speaking to them until he sees the transformed Garmadon. The prison soon comes under attack by Chen's Cultists as Kai, Jay, and Cole fight them while the others realize Pythor holds the key to keeping the spell permanent. Wu and his family escape to make sure Pythor doesn't fall into the Cultists' hands as the Ninja keep them busy, as the prison is put on lockdown.
The fight soon causes the release of the prisoners and Cole break through the walls since the metal door can't be broken. The Ninja run through the prison with the inmates following them and make it to the courtyard finding the Garmadons fighting the Cultists. Kai inquires if they had Pythor as Wu finds that the Cultists have made off with him. To ensure the prisoners don't escape, Wu stops Cole from breaking anymore walls and Zane creates a trail of ice for then to run out of the prison, which Kai destroys so the prisoners can't pursue them, leaving the inmates to be taken back to their cells by the warden and his guards.
They return to the Samurai X Cave, where Nya tells them Chen has shipped out several noodle trucks that could hold swarms of Anacondrai Cultists. The Ninja contact their allies to stop them before their arrival but the trucks separate into going off to other directions, where Misako states there are several villages.
The Ninja and the Elemental Masters summon their Dragons and each pursue a truck, with Kai following one through the city, managing to damage it and capture the driver. Kai opens the truck only to find it empty as he realizes too late that Chen tricked him and his friends to splitting up. The fear that he put many people in danger causes him to lose control of his dragon, leaving him unable to do anything about it.
Kai and the other elemental masters are scattered all around Ninjago, after chasing down the decoy trucks. Nya attempts to contact them from the new Destiny's Bounty. Lloyd instructs Neuro to send a message to the other elemental masters ordering them to Nya's Samurai Cave, 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 Kai going to the comic store for help.
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 hovered into the portal, which then explodes after closing off, ending the war.
The Ninja and the elemental masters then celebrated their victory, with Kai and Jay being hugged by Karlof as they all promise to offer their new friends aid in the future as they part ways.
Later, Kai ask Skylor to join the team but said that she has the noodle-business to run and they almost kissed they get interrupted by Dareth. They part ways although Skylor promised to Kai that she will keep in touch with him.
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.