When the Time Twins fought the Ninja with their army of Vermillion, Zane helped the Ninja strategize against their adversaries. Though they were ultimately defeated, Zane lost contact with P.I.X.A.L. in the ensuing conflict.
The Ninja are cleaning up the museum when Nya finds the painting of her and Kai's parents. After reflecting on their past with their parents, Cole ushers them to check out another painting they found, which was of the battle where the Elemental Masters fought with Krux and Acronix. Cole asks if anyone recognizes the battle, and Zane asks P.I.X.A.L. to analyze it. She tells them that the battle took place 40 years ago during the Serpentine Wars. Then, when Dr. Saunders comes in to offer the Ninja refreshments, Lloyd asks about the painting. Saunders calls it "minor skirmish" and tells the Ninja that it has no historical significance, which prompts Zane to tell ask him "Even if it is a myth, who are these men Masters Wu and Garmadon supposed to be fighting?" Dr. Saunders tells them about the Hands of Time, and how they can manipulate time, and their names: Krux and Acronix.
Following the Fast-Forward Blade's arrival at the Monastery, and time skipping an entire minute, the Ninja are sent from running out of the museum, to standing at the bridge of the Destiny's Bounty 2.0. With alarms going off all around them, the Ninja are wondering how they ended up there. Zane mentions that his circuits are picking up an energy displacement. Zane and Nya then try to figure out the location of the energy displacement, while Jay freaks out about the noises in the background. They find out that the energy displacement is temporal energy, and is coming from Wu's Monastery. After remembering that Wu is there, they decide to check it out.
They go there and find Acronix fighting with Wu. They step in, and "defeat" him, but Acronix merely used the Time Blade to warp away. The Ninja find Wu holding on to a tree branch about to fall, and help him up.
The Ninja have returned to the Temple of Airjitzu to rest Wu, and ask him questions about who they just fought. Wu tells them all about Krux and Acronix, before he fell asleep which left the Ninja having nothing to do anymore. While they're cleaning up the Temple, they see on the News that a samurai warrior (A Vermillion) is attacking the Borg Store. They race down there to find out who will fight him first, and when it ends up being a tie, they ask Zane to use his digital die to decide. Each of them gets a chance fighting the Vermillion, but it's too strong for one at a time so they all fight at once. The fight continues into the store, and Zane finds out that the Vermillion is trying to kidnap Cyrus Borg, so he takes him away from the fight and into an alleyway before Borg sees Dr. Saunders, and asks him why he's there before Zane is suddenly struck down.
After dealing with the Vermillion, the Ninja find Zane unconscious in the alleyway, alone.
After asking Master Wu about the Vermillion, the Ninja (except for Kai, who went to the museum to ask Dr. Saunders about the Vermillion) meet at the Samurai X Cave to figure out how to reboot Zane. After trying multiple times, and nothing works, a video of Zane's last moments awake plays on the screen. After replaying it, and slowing it down some more, they realize that Acronix was the one that disabled Zane, and that Acronix and Saunders are working together. The Ninja leave Zane in the X-Cave on a restore and reboot protocol so they can go warn Kai. As they leave, P.I.X.A.L. appears on the screen above Zane, and tells him to wake up and that Kai needs them.
The Ninja return to the X-Cave after finding out that Saunders is actually Krux, and finally reboot Zane. He wakes up without leaving the bench and says the numbers "4721" in that order before falling back asleep.
After rebooting Zane's system, Nya thought she succeeded, but found he was only speaking gibberish. P.I.X.A.L. tries to explain to Nya that she's trying to unscramble Zane's neural pathway, unaware that's causing him to speak nonsense. Nya then left to retrieve a binary power cord, much to P.I.X.A.L.'s dismay.
After a confrontation with the Vermillion, Nya came back to the cave but found Vermillion trying to take Zane's metal. She fended them off, but Zane was unable to fight. P.I.X.A.L. sent the electricity to his chest, shocking the Vermillion, and killing them. Nya took Zane with her back to where the Vermillion were stealing metal from buildings.
The Ninja stop the Vermillion, and try to find a way to get Zane's power back, and they figure they can go to the Power Plant. At this time, Lloyd also goes there to meet the Ninja. When they arrive, they enter to find no Vermillion inside. Zane says something in gibberish, and Nya translates that there are Vermillion all around them. They start to fight them (except for Zane, who is walking into a wall.) Nya and Jay find the main core, and hook Zane up to it after defeating the Vermillion, and do something that causes Zane to reboot, and return to normal. The others fill him in on what's going on, and see on the news that Mega Monster Amusement Park is being invaded by Vermillion. The Ninja leave to the Park (except Jay, who goes to make sure his parents are ok.) Before they drive away, Zane asks P.I.X.A.L. something, but she does not respond.
Zane and the other Ninja are fending off Vermillion in Mega Monster Amusement park, when they are cornered, which prompts them to wonder where Jay is, as he had disappeared.
Jay finds his parents in trouble with the Vermillion at their Junkyard, when the second Time Blade arrives. The Vermillion takes Edna, to go after it, and Jay tries to go after her but his bike was broke. His father gives him his early birthday present which is an early version of the Desert Lightning that breaks down when touched, so Jay fixes it up and goes after the Vermillion. Meanwhile, the Ninja go after the Vermillion who left the Amusement Park. Before they leave however, Zane starts reciting the numbers 34 and 28. The Ninja assume he is knocked offline again, but Nya tells them that he was referring to latitude and longitude. Zane recalls that Nya updated her Temporal Scanner, so now he knows the Time Blades location, which is in the Eastern Sea of Sand. They take off on the Ultra Stealth Raider. The Ninja and Zane meet Jay chasing the Vermillion, while attempting to retrieve the Time Blade before them. In the chase, Zane and Nya are knocked off their Ultra Stealth Raider bike, as well as the other Ninja, so now they run after the Time Blade on foot.
After a quarrel with the Time Blade being possessed by the Vermillion, the Ninja finally retrieve it and escape by slowing down the Vermillion and then flying away on what was left of the Ultra Stealth Raider Jet, while Zane helps stabilize the wings.
After returning back to the Temple after retrieving the Time-Blade, Cole, Zane, and Jay are relaxing by fooling around with the blade. Cole accidentally almost hits Nya in the head with the Blade, and she tells them to cut it out. The three boys mention how she's been trying to locate her Samurai X Suit, since it was apparently stolen by the Vermillion, and also how Kai has been reading through many history books to, unbeknownst to them, figure our where he's seen the symbol under the Vermillion's helmet before. Kai says something about finding a clue, and the others return to playing with the Time Blade. Cole and Jay proceed to run at each other, while Zane slows them down. Lloyd enters in the middle of this, and reminds them that they should have hidden it. Cole makes fun of Lloyd, and Wu enters saying the same thing word for word, plus how they should not let victory cloud their vigilance. As he finishes talking and starts walking away, a Vermillion egg crashes through the window. The Ninja discover that outside, the Vermillion are all lined up and ready to attack. They get into battle with the Vermillion, and one Buffmillion. The Vermillion still attack, so Lloyd tries to defeat the Vermillion on the ground. During this time, the Destiny's Bounty is attacked, and it crashes to the ground. The time twins later intervene and fight the Ninja, and Wu and the Ninja end up taking the Fast-Forward Blade. At this time, the Samurai X Mech steps in to help. Nya thinks that the Vermillion stole her suit, but it turns out that the new Samurai X is no Vermillion, however, they refuse to reveal their identity. Sam-X flies away but is knocked out of the sky by an egg. Now, the Ninja fight the Time Twins, and they think they've won, but General Machia swoops in from the air and steals both Time Blades, and returns it back to the twins. Before they escape, Machia kidnaps Wu.
At the Temple, Lloyd is giving a pep talk to the Ninja about how even though they lost, it can be good thing that they took the time blade because then they can follow the Hands of Time back to their base. The Ninja split up and Kai and Nya go to the Destiny's Bounty to see if the Temporal Scanner works. Cole and Jay go with Lloyd and Zane who take the Destiny's Shadow to the museum to find any clues. While on the Shadow, Zane asks P.I.X.A.L. a question, but then remembers that she is still "offline". Zane, Jay, Cole, and Lloyd search the museum for anything, all the while, Jay is throwing artifacts all over, which leads Zane to tell him to stop, as he catches everything he throws. Lloyd comments on how he's glad Zane is fully functional, and he agrees, except for the fact that he can no longer talk which P.I.X.A.L. which angers him. Then, Cole accidentally punches a hole in the wall which leads to a secret room off of the museum. They enter, and find Vermillion eggs incubating in a tank. Off of the secret room is another secret door that leads to the sewers. They enter the sewers and Zane reconfigures the Destiny's Shadow to float on water. It picks them up, and they use it to navigate the sewers. Along the way, they meet Skales and his son who tells them that they're tracking the Vermillion in hopes to avoid them. They tell the Ninja that they're the spawn of the Great Devourer, and that they are very powerful if they are a horde. He also tells them that their base is in the swamp, and gives them a map that lead there. They reach the swamp, and call the rest of the Ninja to meet them there.
When Kai and Nya arrive at the swamp, they make a plan to rescue Master Wu, and Cyrus Borg. They split up, Zane is to use his scanner to find Borg. Zane locates Cyrus Borg, and moves toward him. Moments later, the signal disappears, which causes Zane to fall to his knees and sulk about how P.I.X.A.L. is gone and that it's "no good". After sulking for a few minutes, Zane's scanners pick up Borg's signal once again. He runs towards it and meets Lloyd halfway. Lloyd tells him that he found Wu, but lost him again. Zane consoles him, and then picks up Jay and Cole's signal. Lloyd and Zane hear them yell, and meet them battling the Vermillion, so they help out. They appear to finish them off, and see the Time Twins in the air wit Wu, Ray, Mia, Kai, and Nya. They begin to Airjitzu after them, but Blunck and Raggmunk ambush them with more Vermillion.
Zane, Cole, Jay, and Lloyd make a "strategic retreat" because they can't handle all the Vermillion. Zane covers them with Ice so they can escape, but he picks up Borg's signal again and he says he's going to get him. The others join him in avoiding the warriors and escaping. When the Vermillion realize that the Ninja have gone, they all go back to their main base which is unfortunate for the Ninja because they need to go there too. Lloyd suggests they disguise themselves as Vermillion in order to enter, and it works. In the entrance of the dome, they meet Cyrus Borg and they get him to escape. First, Jay asks why the Twins kidnapped him in the first place. He reveals that they were making him create the hub for the Iron Doom, that would be used for time travel. He tells them that with all four time-blades, it will be active. Borg tells them that he put in a self-destruct code so that they could stop it, but he did not have the time to enter it in so they had to do it now. Borg tells them that they have to sneak in (to the dismay of Jay). Just then, Blunk and Raggmunk enter and order the disguised Ninja to escort Borg away from the Iron Doom, but Jay breaks character which causes their identities to be revealed. They get into battle with the Vermillion once again, and this time, the new Samurai X shows up with new armor and starts to help them. They battle, and Borg tells Sam-X that he needs to get to the Iron Doom, so they bring him to the top to input the code. Zane uses airjitzu to fly up with them, and helps Borg remember the code, which is the first line of code for programming a nindroid. They are about to finish the code, when the Time Twins return with all four Time Blades. They use the pause blade to stop Zane from finishing the code, and order the warriors to enter the Iron Doom. They enter the TimeBlades into the Iron Doom, and push Zane, Borg, and Sam-X off the platform. Zane falls and Cole catches him. They watch now, as Kai and Nya use the Fusion Dragon to enter the same portal the Time Twins do.
The Ninja sulk about how Nya and Kai had just travelled back in time, and are introduced to Ray and Maya who tells them that the only way to help Master Wu (as he had been hit with a Time Punch, that causes him to rapidly age) is to get the Reversal Blade back. During this time, Jay tries to figure out Samurai X's identity, but they refuse once again.
Krux and Acronix had gone back in time to change Ninjago so that there was no more technology. They briefly accomplishes this, which caused Zane's form to change back human in present day.
After Kai and Nya stopped the Time Twins, and Wu sacrificed himself on the Iron Doom, the siblings return to present day Ninjago, where Zane has returned back to titanium.