Kai and his friends come to the aid of Master Wu when faces off against a villain who can control time with a mysterious gauntlet. Later said man and his brother lead an army of Serpentine with armor with craftsmanship leave Kai thinking about his parents. Kai's search for answers leave to uncover dark secrets about his parents' disappearance.
When the Ninja clean up the museum, Kai told Nya about a picture he found of their parents. Later, they see another picture of Garmadon and Wu forty years ago, and ask Dr. Saunders what it is.
When they're off, an energy displacement caused them to be relocated on the Bounty. P.I.X.A.L. told them the source is at the monastery, where Wu was, and the Ninja took off.
They eventually encountered Acronix and fought him. Afterwards, they save Wu before he could fall off the mountain.
The Ninja asked Wu about their fight with Acronix. Afterwards, they left him so he could rest. They discussed the painting they saw on the museum and how it relates to Wu's flashback.
After a while, the Ninja watched a news channel reporting a Vermillion Warrior wreaking havoc at the BorgStore. They decided to attack it one-on-one, but failed, noticing the Warrior could regenerate. Coming to the conclusion that the Vermillion might try to kidnap Cyrus, the Ninja tried to help him. However, they found Zane unconscious and Cyrus Borg missing.
After failing to figure out what the Vermillion helmet does, they went to see Wu for answers. He was unable to answer, however, so Kai went to the museum while Lloyd stays with Wu and Jay, Cole, and Nya went to the Samurai X Cave to reboot Zane.
When he got there, he asked Dr. Saunders about the helmet, and then decided to look around for anything useful. He discovered Dr. Saunders was Krux, and started attacking him when Nya came to help.
They went back to the Cave, and found Zane rebooting.
After Kai was distant from his previous encounter with Krux, he started to take his anger off on some Sparring Bots. He agreed to fight the Vermillion, but was interrupted when Lloyd told them he will be their new Master. However, when Lloyd suggests they make a plan, they reluctantly agreed.
When Ronin and Dareth came to tell them the Vermillion are stealing metal, the Ninja left.
After a brief fight, the power went out and the Ninja met Lloyd at the power source. They created a magnet to attract the snakes' armor, rendering them vulnerable. The power went back on, and they heard the Vermillion are attacking Mega Monster Amusement Park. They left for the park, and Kai told Nya he needs to tell her something when it's over
Kai fought the Vermillion at Mega Monster Amusement Park. When he sees a symbol on the Vermillion's helmet, he looks at it in astonishment. When he grouped up with the others, they realize they haven't seen Jay since they left for the amusement park.
When time slowed down, the Vermillion Warriors left the park. They figured another Time Blade has arrived, and Zae gave out its location. They left and try to get there before the Vermillion do.
Nearing the Time Blade, Raggmunk threw snakes at them to make them crash. When they tried to get it, Blunck shot them with the Time Blade, slowing them down.
The Army and Ninja were slowed down right when Jay came to save them. He managed to free everyone from the time bubble. They fought for the Blade and managed to escape with it.
After closely examining the helmet, Kai states he's got a clue, but it turned out to be false and he continues to observe it.
When Wu told the Ninja to net let pride cloud their judgement, Kai asks Wu what the symbol meant and asked for everything he knew.
A moment later, they were attacked by Vermillion. They defeated them with Spinjitzu, and Kai asks Wu what the symbol meant. The snakes regenerated into Buffmillion, and Kai and Nya tripped it until it fell down the floating island.
Lloyd suggests they take out their weaponry by using their Dragons, but they don't think it's a good idea. Lloyd's Dragon disappears and Kai tries to save him, but was held back by the Vermillion's sky team. Samurai X saved Lloyd, but flew away before anyone could find out their identity.
Just as Wu was about to answer Kai's question, they were confronted by the twins. They eventually got both the Blades, but it was stolen by Machia when they least expected.
They mourned over their defeat and blamed their overconfidence.
Seeking council, Kai journeyed to Mr. Chen's Noodle Shop to speak with Skylor, as she had dealt with her father being a villain as well. Nya soon arrived and he presented the two helmets as evidence to her, though he was met with skepticism until he proved it to her. The siblings realized their father was still alive but couldn't bring themselves to accept he is working with the enemy. They were soon interrupted by a call from Lloyd, informing them that the other Ninja had discovered the secret base of the Hands of Time. As he and Nya set out, Kai realized that this meant they also knew where their parents were.
Kai entered the blacksmith's building and found his father Ray building weapons. Kai confronted him and attacked the latter as the latter defended himself. Kai then revealed his identity to his shocked father who tried to talk him down but he didn't listen to him nor his arriving sister. However, the voice is his mother Maya and he stops but still tells Nya she is guilty like their father. Their parents proceed to tell them the truth: Krux wanted revenge on them for building the Time Blades and threatened Kai and Nya if they didn't comply which is why they were separated. Hearing this, Kai felt guilt for accusing them as he sees they weren't at fault.
When Kai refused to retrieve the Time Blade for the twins, Nya reminded him it's the only way to save Wu. Later, when Ray gave them the Dragon Blade to create the Fusion Dragon, Kai's impatience caused them to miss out on Ray's advice. Once inside, Nya creates a water slide to reach Hono Mizu.
When they reached the bottom, they were greeted by Geoatomic Rock Monsters. When they used both their powers together, they realized they needed to work together. Once they reached a door, Nya figured out they open it with the Dragon Blade. When Kai took the Blade, however, the building starts to collapse. They used the Fusion Dragon to escape.
Once they returned, Kai was about to use the Time Blade on him but the twins said they lied about their promise. As they fought, Ray pushed Kai so he would be hit with the Time Punch instead. Acronix used the Pause Time Blade on everyone and they stole the Reversal Time Blade and left with the ship. When they let them fall into the Boiling Sea, Nya and Kai used the Fusion Dragon to save everyone.
They went to the Iron Doom, with Ray and Maya jumping off to increase speed. They followed the Iron Doom into the Temporal Vortex.
As the Iron Doom traveled to the future, Krux complained to Acronix about going to the future. Acronix tells him that by going into the future, there would be no one who recognizes them, no Elemental Masters and no Kai and Nya.
At that moment however, The Hands of Time are confronted by Kai, Nya and Wu. Kai taunts them for being wrong as the final battle between them begins, Acronix fights Nya and Wu while Krux fights Kai. After Nya leaves to help her brother in fighting Krux, who they proceed to overwhelm until Acronix joins in to aid his brother.
As the Iron Doom began to pass by the present, Acronix and Krux were able to overwhelm Kai and his sister and were about to finish them off, but are stopped by Wu. As Acronix tells him there is nothing he can do, Wu then proceeds to rip out the Reversal Time Blade from the Time Apparatus, causing the Iron Doom to spin out of control. Kai and Nya fall as Wu gives them the Reversal Time Blade before they returned to the present so that they can cure their father of the time punch. Wu stayed behind confronts a defeated Acronix and Krux, saying that it indeed ends now. As the three fought, the Iron Doom became lost in time with them still aboard as it traveled far into the future.
Though happy at their victory, Kai couldn't help but be worried when his master was feared to be lost in time with their enemies. He and the Ninja elect Lloyd as their master and he makes his first order to bury the reversal time blade and to discover what happened to Wu.