Nya and her friends come to the aid of Master Wu when he battles a villain who can control time with a mysterious gauntlet. Later said man and his brother lead an army of new serpentine warriors with armor Kai recognizes and tells Nya their parents possibly made it leading him to investigate. While he does that, Nya learns someone has taken her old Samurai X armor leading her to take on her own investigation and finds out this mysterious person has taken up the mantle for themselves. Later on, she and her brother are reunited with their parents and learn some disturbing details of their past. The two are later forced to help the Time Twins when they threaten their parents
As the Ninja cleaned up the museum, Kai told Nya about a picture of their parents. Later, they saw another picture of Garmadon and Wu forty years ago, and asked 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 saved 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 Cole, Jay, and Nya went to reboot Zane in the Samurai X Cave while Lloyd stays with Wu and Kai goes to the museum.
They discovered a video feed and slowed it down to reveal Zane being hit by something. After slowing down the video more, they discovered Acronix and Dr. Saunders working together. They rushed to the museum to stop Kai, but Jay and Cole stayed behind to battle with the Vermillion Warriors.
They went back to the Cave, and found Zane rebooting.
Nya had told the Ninja to go back to the Temple of Airjitzu while she tries to fix Zane. However, he started speaking nonsense, so she left to get him a new binary power core, much to P.I.X.A.L.'s disappointment.
When she came back, she found him attacked by Vermillion snakes. They were defeated, but she realized her Samurai gears are gone.
She and Zane went to tell the Ninja about the Vermillion and helped fight them.
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.
As she fought the Vermillion at Mega Monster Amusement Park, Nya questioned who stole her Samurai X suit. When she 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. However, they are freed right before the Vermillion could attack them.
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.
The Ninja were at the Temple of Airjitzu where they discussed their next move before the Vermillion attacked them. When the twins landed on the temple, Wu battled Acronix with the Slow-Mo Time Blade which slowed Time on him, however, Krux got the Forward Time Blade and battled Wu and the Ninja. Eventually, Lloyd got the Forward & Slow-Mo Time Blades, but the victory was short-lived as Commander Machia arrived and retrieved both Time Blades from Lloyd's hands, and she and the Hands Of Time escaped with the Time Blades and Wu.
Nya was jealous that someone stole her old armor and wanted to best the new Samurai X. She later returned to the Samurai X Cave where she found the mysterious new samurai.
Nya returned to the Samurai X Cave where she found the new Samurai still lurking. Still angered about the theft of her suit, Nya attacked the warrior and the two engaged in a battle throughout the cave. However, the mysterious figure used a voice scrambler and as their fight continued, it attempted to assume the identity of multiple people including Ronin, Dareth, Misako, and even Garmadon. However, it was only when the new samurai took on Nya's own voice in an attempt to convince her of the importance of keeping its identity a secret. Realizing it was time to pass the mantle onto a worthy successor, Nya yielded. She presented the Samurai VXL to the new warrior, but was then summoned to Chen's Noodle House by Kai.
Upon arriving at the Noodle House however, Nya was horrified to find Skylor present, thereby ruling her out as the possible new samurai. As she took a seat, Kai revealed to Nya that he had found an old Vermillion helmet back at Four Weapons, thereby proving that their parents worked for the Hands of Time. Before they could talk further however, Nya received a call from Lloyd informing her that the other Ninja had found the lair of the Hands of Time. As she and Kai set off towards the coordinates, Nya realized that this meant they were also heading to where their parents were.
Nya and 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 his attack. Nya embraces her mother, stating she missed her but Kai 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, Nya was horrified as her brother felt guilt for accusing them as he sees they weren't at fault.
As Ray and Maya told them to flee, the Time Twins appeared having overheard a conversation between Ray and Maya and their children Kai and Nya and they quickly revealed themselves after discovering Ray and Maya had hidden the Reversal Time Blade 40 years prior on the orders of Wu. They brought Kai, Nya, their parents, and Wu onto the airship, using this as leverage against Kai and Nya to retrieve the reverse blade, promising if they do, they can save Wu.
Nya reminds Kai they need the Blade to save Wu from the Time Punch, and they both agreed to retrieve it. 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.
When Nya and Kai were about to save Wu, the twins intervened and prevented them from doing so. 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. Nya joined her brother in taunting the villains for being wrong as the final battle between them begins.
Nya and Wu fought Acronix while Krux fought 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 Nya and her brother 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. Nya and Kai fell out 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, Nya couldn't help but be worried when her master was feared to be lost in time with their enemies. She 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.