Hands of Time

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 Ninjas 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 Ninjas 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, the Forward Time Blade arrives through the vortex and Acronix uses it to hit Wu with a time punch that accelerates his aging. During the ensuing battle, Acronix reveals that he knew Kai and Nya's father and then escapes after faking his own demise. He then meets up with Dr. Saunders, who is revealed to be none other than Krux.

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 Vermillion warriors, humanoid warriors made up of snakes, joined together in suits of armor. One is sent to abduct Cyrus Borg at his new product launch, and two more are unleashed when the Ninja arrive to save him, with Acronix and Krux abducting Borg after Zane tries to take him to safety. The Vermillion keep the other Ninja occupied. The ninja attempt to fight the Vermillion but discover that they can immediately reform upon defeat.

As Acronix and Krux unleash more Vermillion, including the three commanders, General Machia, Blunck, and Raggmunk, and task them to kidnap various craftspeople from around the city. The Ninja split up in an effort to determine the source of this new menace. Cole, Jay, and Nya take the inactive Zane back to the Samurai X Cave for repairs 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. Nya arrives to back Kai up against the Time Twins, but the villains escape with Cyrus Borg using the Time Blade Acronix used against Wu.

Wu confesses to Misako that Acronix's attack has accelerated his aging process, and tells her to keep it secret, while Nya continues her attempts to repair Zane, frustrating Pixal with her lack of progress. With Wu out of action, Lloyd tries to rally the Ninja, 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 a still malfunctioning Zane. In an effort to prevent their interference, General Machia sends a group of Vermillion to cut power to Ninjago City. The Ninja, joined by Lloyd after a talk with Wu restore power, and head to Mega Monster Amusement Park to confront the Vermillion. A repaired Zane notices with concern that Pixal is not responding.

While the rest of the Ninja, face off with the Vermillion at the amusement park, Jay goes to the aid of his parents as their scrapyard is also invaded. The arrival of a second Time Blade, a time-slowing 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 brother, Krux who hates technology. Two groups of Vermillion Warriors set out, with the scrapyard group, who also abducted Jay's mother and stole a large supply of metal, reaching the Time Blade first. Its powers allow them to hold the Ninja at bay until Jay arrives on his new bike, which he and his father built. The Ninjas succeed in recovering the blade and escaping, 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 recognizes the symbol branded in a previously retrieved helmet of a Vermillion Warrior, but before he can elaborate, the Temple is attacked. As his teammates engage the Vermillion, Lloyd joins the battle using his elemental dragon, only for it to dissipate due to his fear. He is unexpectedly saved by the Samurai X Mech, previously thought stolen by the Vermillion. Both the mech and the Destiny's Bounty are shot down, and the Hands of Time succeed in capturing the Time Blade and abducting Wu.

With the Bounty wrecked, the Ninjas are forced to take separate vehicles as they set out to locate Wu and their enemies. Misako also reveals that Wu is rapidly aging, and Kai realizes that the mark on the Vermillions' helmets is his father's blacksmith brand. 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 Nya returns to the Samurai X Cave, where she finds the person who stole her armor. Though the thief doesn't reveal their identity and changes their voice to sound like different people, Nya is convinced by their conviction and skills (and the mistaken belief that the person is Skylor) to pass on the mantle of Samurai X to them. Meanwhile, the other four Ninjas search the sewers of Ninjago for the Time Twins' lair after discovering their lab and encounter Skales, who reveals that the Vermillion are the progeny of the Great Devourer.

The reassembled, Ninja team venture into the underground swamp where the Vermillion Warriors have been bred, in order to rescue Wu, Cyrus Borg, and the kidnapped workers. Kai is determined to track down and confront his father, Ray, while Zane, still struggling with P.I.X.A.L.'s absence, searches for Borg, and Lloyd goes looking for Wu. While the Time Twins are busy retrieving the third Time Blade, Cole, and Jay find the prisoners, including Karlof, Lou, and the Royal Blacksmiths. Lloyd finds Wu under guard by Raggmunk and Blunck, who are bemoaning Machia's recent promotion over them but fails to rescue him. Kai confronts his father, believing him to be a traitor, only to be stopped by his mother and Nya. The siblings learn that Krux, after returning to Ninjago alone, forced their parents into aiding him against their will. It is soon revealed that the Time Twins' plan involves a weapon known as the Iron Doom, built using Ray's metalworking, and Borg's technology, that can use the power of the Time Blades to travel through time. Before they can act to stop it, the Time Twins and their forces return and force Kai and Nya to help them to retrieve the final Time Blade from its hiding place.

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 a dangerous environment, where they face numerous obstacles. Meanwhile, Lloyd and the others set out to rescue Cyrus Borg, who installed a self-destruct feature on the Iron Doom. In an ensuing battle with Blunck and Raggmunk's Vermillion warriors, the Ninja are joined by Samurai X, who hacked into Zane's sensors to track them down and also seeks to rescue Borg. 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 are saved by the Fusion Dragon. The Time Twins return to their base, and after thwarting Borg's sabotage order all their forces into the Iron Doom, which then enters a temporal vortex with the Fusion Dragon in hot pursuit.

Left in the present, Maya and a rapidly aging Ray meet up with Borg, Samurai X, and the remaining Ninja while Kai and Nya, and Wu have boarded the Iron Doom, which soon arrives in Ninjago's past just after the Time Twins' original defeat, and unleashes the Vermillion on the victorious Elemental Masters. Doing their best to mitigate any damage to the past without causing more, Kai and Nya impersonate their parents to join a young Wu and his allies in battle, but the Vermillion snakes merge with Iron Doom itself, animating it, and allowing it to defeat the past Elemental Masters, resulting in a present where no technology exists. Kai and Nya form the Fusion Dragon once again to attack, but Kai is defeated after Nya leaves for unspecified reasons. The Hands of Time decide to depart for the distant future so that they won't have to continue dealing with their interference. Having found the Reversal Blade in the past, prior to it being hidden in the Boiling Sea, Nya uses it to restore Wu's health, and with Kai's help, they use it to reverse time, enabling them to board the Iron Doom while leaving the Reversal Blade with young Wu. A battle aboard the Iron Doom ends with Wu removing the Reversal Blade, which sets the Iron Doom adrift in time, and giving it to Kai and Nya, who are then dropped in the present where they use it to save their father. With Wu having been lost in time, staying on board the Iron Doom to fight Krux and Acronix, Lloyd is declared the new master.