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.
Kai is surprised when the man revealed that he knows his father.
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.
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.