At the ruins of the Monastery of Spinjitzu, a strange vortex opens up to admit a mysterious hooded warrior who is then confronted by Master Wu; the pair recognize each other and Wu reveals that it has been forty years since he last encountered his enemy. Elsewhere, Misako is unloading supplies at the Temple of Airjitzu with the assistance of Ronin and of Dareth, while the Ninja are helping Dr. Saunders at the museum. While there, Kai and Nya find a portrait of their long-missing parents, Ray and Maya, and the Ninja also discover a portrait of a battle between Wu and Garmadon and the "mythical" Hands of Time, Acronix and Krux. Acronix, who happens to be Wu's mysterious enemy, is defeated but then restarts the battle after a Time Blade emerges from the vortex, causing a temporal wave that draws the Ninja to the monastery after Acronix strikes Wu with the weapon. During the ensuing battle.

Wu, still recovering from his battle with Acronix, reveals to the Ninja that the Hands of Time were once Elemental Masters of Time who turned on their comrades after the Serpentine Wars. After a series of battles, their powers were drained into the four Time Blades, which were then sent into the time vortex and followed by Acronix and Krux themselves. Believing both to have been destroyed, the Ninja set to work unpacking their belongings into the Temple of Airjitzu, with Nya expressing some regret over leaving behind her Samurai X costume. Meanwhile, the reunited Acronix and Krux embark on their plan to conquer Ninjago, which involves unleashing the sixth tribe of Serpentine, the Vermillion warriors, snakes who join together inside armor to form humanoid warriors. One is sent to abduct Cyrus Borg at his new product launch, and two more are unleashed when the Ninja arrive to save him.

As Acronix and Krux unleash more Vermillion, including Commanders and Generals Machia, Blunck, and Raggmunk, the Ninja split up in an effort to determine what is behind the latest menace to Ninjago, which includes the kidnapping of various craftspeople from around the city. Cole, Jay, and Nya take the inactive Zane back to the Samurai X Cave in hopes of repairing him, and soon discover that Acronix is still alive and in league with Dr. Saunders. Kai makes the same discovery after visiting Saunders at the museum with a piece of Vermillion Tribe armor, as well as learning that Saunders is Krux. The villain also claims that Kai's parents sided with him and Acronix during their conflict with the Elemental Masters.

Wu confesses to Misako that Acronix's attack on him at the monastery has accelerated his aging process, telling her to keep it secret, while Nya continues her attempts to repair Zane and frustrates P.I.X.A.L. with her lack of progress. With Wu out of action Lloyd tries to rally the Ninja out of guilt for not being for him at the monastery, while Kai continues to struggle with Krux's claim that his parents were traitors. The Vermillion raid Ninjago city in search of metal, and Kai takes Cole and Jay off to confront them in defiance of Lloyd's orders and are joined by Ronin, Dareth, Nya, and Zane, the latter still malfunctioning. In an effort to prevent their interference, Commander and General Machia sends a group of Vermillion to shut down Ninjago City's power, and after a talk with Wu, Lloyd joins his teammates, who succeed in restoring the power.

The Ninja, except Jay, face off with the Vermillion at the amusement park while Jay goes to the aid of his parents as their scrapyard is invaded. However, the arrival of a second Time Blade changes things, with the Vermillion being directed to retrieve it after the technology loving Acronix pinpoints its location using his new Borg Watch, to the annoyance of his innovation-hating brother Krux.Two groups of Vermillion Tribe set out, with the scrapyard group abducting Jay's mother as well as stealing a large supply of metal, and manage to reach the Time Blade first. Its powers allow them to hold the Ninja at bay until Jay arrives with his new bike, which he has put together with help from his father. The Ninja succeed in recovering the blade and escaping on the bike and the Ultra Sonic Raider jet, but Machia and the Hands of Time are determined to take it back.

Having returned to the Temple of Airjitzu, Jay, Cole, and Zane are letting their success in retrieving the second Time Blade go to their heads. While Lloyd fears reprisal from the Time Twins, Kai mulls over the supposed treachery of his parents, and Nya continues to wonder about her missing Samurai X gear. Wu gets up and supports Lloyd's fears.He recognizes a symbol branded in the Tribe of Vermillion helmets that have been retrieved previously. Before he can expand on it, however, the Temple is attacked by the Hands of Time and their Vermillion warriors. As his teammates try to fight them off, Lloyd uses his dragon to attack the forces on the ground, only for it to dissipate due to his fear. He is then unexpectedly saved by the Samurai X Mech, revealing that the Vermillion Tribe were not responsible for the theft of Nya's equipment after all. Both the mech and the Destiny's Bounty are shot down, and the Hands of Time succeed in capturing the Time Blade and Wu before departing. 

With the Bounty wrecked, the Ninja are forced to take separate vehicles as they set out to locate Wu and their enemies.Cole takes the Titanium Tumbler, Jay takes his bike, Kai and Nya take their old bikes, and Lloyd and Zane use the Destiny's Shadow, a flying boat given to him by Misako. Misako also reveals that Wu is rapidly aging, while Kai realizes that the mark on the Vermillions' helmets is his father's blacksmith brand. He and Nya thus set out separately to find answers. He returns to their family shop and discovers a hidden chamber concealing a strange two-bladed dagger and evidence that his parents are alive, while she returns to the Samurai X Cave and finds the thief of her suit, who changes their voice to sound like different people, such as Dareth, Ronin, Misako, or Garmadon. In the end the Samurai's conviction and skills are enough that Nya agrees to relinquish her identity, though she insists on the new Samurai X changing their color scheme; she also comes to believe that Skylor is the one in the armor,.

Having reassembled, the Ninja head into the underground swamp where the Vermillion Tribe have been bred in order to rescue the captured laborers, Wu, and Cyrus Borg, while Kai is determined to track down and confront his father. Zane, still struggling with P.I.X.A.L.'s absence, searches for Borg while Lloyd goes after Wu. Cole and Jay find the prisoners, including Karlof, Lou, and the Royal Blacksmiths. Lloyd soon finds Wu under guard by Raggmunk and Blunck, who are bemoaning Machia's recent promotion over them, and attempts to rescue him but fails. Cole and Jay attempt to rescue the various craftspeople, while the third Time Blade returns to Ninjago and is retrieved by the Time Twins. Meanwhile, Kai confronts his father believing him to be a traitor, only to be stopped by his mother and Nya, and then to learn that Krux, after returning to Ninjago alone, forced them into aiding his plans for conquest.

With no other hope of saving Wu, Kai and Nya are forced to enter the sunken library of Hono Mizu in the Boiling Sea, a volcanic region where their parents hid the Reversal Time Blade. Using their father's Dragon Blade, they combine their elements to form a Fusion Dragon and enter the dangerous environment, where they face numerous obstacles. Meanwhile, Lloyd and the others set out to rescue Cyrus Borg, only to learn that he has rigged a self-destruct feature on the Iron Doom. In an ensuing battle with Blunck and Raggmunk's Tribe of Vermillion warriors, the Ninja are joined by Samurai X, who has arrived seeking to save Borg as well after hacking into Zane's sensors. Kai and Nya succeed in retrieving the blade, only to lose it to Acronix and Krux after Ray is struck with a Time Punch. Kai, Nya, their parents, and Wu are then left falling to their doom but survive by forming the Fusion Dragon yet again. The Time Twins return to their base, and after thwarting Borg's sabotage order all their forces into the Iron Doom.

Left in the present, Ray and Maya meet up with Borg, Samurai X, and the remaining Ninja while Kai and Nya have boarded the Iron Doom with Wu in hopes of stopping the Time Twins and retrieving the Reversal Blade. The villains' plan is soon revealed as the Iron Doom arrives in Ninjago's past just after the Time Twins' original defeat at the hands of the Elemental Masters, who are soon attacked by the Vermillion. Doing their best to mitigate any damage to the past without causing more, Kai and Nya then impersonate their parents to join young Wu and his allies in battle, only for the Vermillion snakes to merge with Iron Doom itself and give it the power of motion. They soon achieve victory over the past Elemental Masters, resulting in a present where no technology exists and where Ray's health continues to deteriorate as he ages rapidly. Kai and Nya form the Fusion Dragon once again to attack, but Kai is defeated after Nya leaves on an unspecified errand. However, the Hands of Time decide to depart for the distant future so that they won't have to continue dealing with their interference.,