A year after Wu was lost in time, Lloyd has taken up the role as master and continues the search for his uncle while his mother Misako, went to go look for him, not telling anyone. Lloyd and the others deal with a group called the Sons of Garmadon who want to resurrect his father's evil side to submit the city and Lloyd meets Princess Harumi who may not be all she claims to be.
Lloyd attempts to stop a raid where six robbers steal an ancient mask. With P.I.X.A.L. as his guide, Lloyd pursued them, only able to stop one and left him to be arrested, but failed to stop the others, choosing to reunite the team. As they meet up, a man named Hutchins says the stolen mask is an Oni Mask. He also tells them he is head of security to the Emperor and Empress of Ninjago and wants the Ninja to assist.
Lloyd discovers someone in Princess Harumi's room and pursues them, only to find it was Harumi herself, making a small run to feed homeless kids. In order to escape Hutchins, Harumi gives Lloyd a hoodie before they move across town and hand out the food. Later, they talk on a bridge about their lives before noticing some punks harassing some kids, Lloyd quickly recognizing them as the Sons of Garmadon. After Samurai X scared them off, Hutchins catches the two and escorts Harumi back to the palace himself. Lloyd later eavesdrops on Harumi being reprimanded about the previous night by her parents before they exchange apologies and Hutchins, catching him eavesdropping tells Lloyd to stay away from Harumi.
Since their headquarters was too out in the open, they decide to stay on the Destiny's Bounty. Before heading to question the suspect Lloyd stopped, they visit Mistaké for the Tea of Truth before noticing a painting and wants to learn about it.
Lloyd and Jay stayed behind to hear the Tale of the Oni and the Dragon, with Lloyd learning his grandfather once lived there before creating Ninjago. Mistaké also tells him the Oni Masks will resurrect his father, as a soulless being.
In an attempt to look for Zane and Cole, Lloyd went to Central Station.
Offscreen, Lloyd and the Ninja found Cole, who escaped along with a mysterious baby. Lloyd and the Ninja find Zane, unconscious and bring him aboard the Bounty. Later, Lloyd, Cole, Kai, and Jay tried to calm down the baby as he cried before they try to bet which hood will double as a diaper. But Harumi was able to calm him down by singing to him. He and Harumi later watched a storm cloud called "Dead Man's Squall" before they nearly kiss, but Lloyd chickens out at the last minute. They later discuss the baby's blanket, which was a map to Primeval's Eye, where a friend of his mother's Dr. Yost but never returned. When P.I.X.A.L. confessed to being Samurai X, she was soon hacked by The Quiet One and attacked them. Lloyd and Harumi end up using her mech to escape and in the process, Lloyd broke his arm and Harumi uses the blanket as a sling for him.
As they moved through the jungle, Lloyd was soon dragged by a creature, unintentionally straightening his broken arm before Harumi rescues him and kisses him on the cheek before they continue on. They soon find a boat with the Sons of Garmadon insignia on it and take it down the river. As they move along it, Harumi asked if Lloyd wanted to see his father again. The Green Ninja and master told her how he had the greatest villain as his father, considering it an unusual relationship. But soon, they were stalked by a creature and when Lloyd tried to fight back, the thick hide of the creature ended up breaking his sword before they soon go over a waterfall and find a cave, leading to the third Oni Mask.
Lloyd and Harumi go into the Oni Temple to find the Mask of Hatred, with the latter "accidentally" setting off a trap before finding the mask.
Since Harumi was unable to grab it, Harumi lets it slip that she knows that only someone with Oni blood can grab it. Lloyd grabs the mask and Harumi congratulates him but this results in him realizing that she is The Quiet One. Harumi admits to this and tells Lloyd her reason for resurrecting Lord Garmadon, calling him the real hero as he destroyed the Great Devourer, mocking the Ninja for their failed efforts while also revealing to him that his uncle Wu was really the baby, to his great shock. He tries to stop her from making a grab for the mask, but she puts it on and turning gray.
After leaving Lloyd trapped in the chamber, she sets off another trap, resulting in the temple flooding in attempt to drown Lloyd. She later reunited with her comrades and they try to escape when the Ninja surround them and she taunts them over their previous belief in her before Lloyd was able to get out the cave and the creature from before attacks them.
Realizing the Ninja are distracted, the Sons of Garmadon use this to their advantage to take the Destiny's Bounty and flee with the masks. Lloyd comes to stop them, but is captured by Killow and the Sons of Garmadon.
Lloyd was brought up to the Temple of Resurrection that was among the ruins of the palace, teasingly pushed by Killow beforehand.
At the center, he was reunited with Misako and told by Harumi that she never had feelings for him before they were both were placed in a counter cell where if one cage is raised, the other is sent underwater to awaiting piranhas. The Ninja soon arrived and freed Lloyd where they stopped Harumi by using Spinjitzu.
As the members and Harumi were arrested, Lloyd hugged his mother after she was freed by an officer. As the cops praised them, Lloyd stops one from closing the back of the transport van where Harumi was.
In retaliation for her betrayal, Lloyd saw through a lie she made, saying he was right and it wasn't her who got away, he used her own words against her before closing the doors on her before the van drove off.
As the Ninja celebrate at Dareth's bar, Lloyd doesn't feel like celebrating, due to Harumi breaking his heart before being comforted by his mother. Upon seeing the news on TV, he tells Dareth to stop the music, ruining the other Ninja's singing as they see a report on Harumi's breakout. He has Dareth take Misako and Wu to a safe place (Dareth's Apartment) while they go see the injured officers. The Commissioner says the one who broke her out was Garmadon and that he was no longer the man he recognized. They soon hear breaking news that Harumi and Garmadon have taken over Kryptarium Prison and released the Sons of Garmadon.
Although he wanted to try and reason with his father, the other Ninja object, so he disables the navigation system, locks the Ninja and P.I.X.A.L. in a room and takes off for the prison. As soon as he arrived, they decide to broadcast his presence on all TVs to Ninjago as well as the fight between him and his father. Lloyd tried to reason with his father, Garmadon doesn't listen as there is no more good in him before throwing him through a wall, into a locker room, where he starts having difficulty breathing. The barely breathing Lloyd was unable to keep fighting and was knocked out of the prison. He was left on the ground, weakly breathing before losing a photo of himself and his father back when he was still good.
Lloyd was given some Tea by Mistaké and the help of the Ninja to get back on his feet. He lost access to his powers, however.
As soon as he was on his feet, Lloyd and Nya were about to head off to rescue Wu and Misako as Garmadon will go after them. After listening to Mistaké's advice about power as well as a gift from her, they took off. They made it to Dareth's apartment where Misako had Lloyd take Wu while she and Nya hold off Garmadon. They were soon confronted by Harumi, wearing the Mask of Hatred and took off. When they end up at a dead end, Harumi appeared and offered him a position in her gang, but he refuses before jumping onto a tram.
Managing to get Wu to his friends before Harumi grabbed him, she forced him to watch Colossus crush the Bounty and killed his friends and uncle, completely unaware that they survived, via Traveler's Tea. Stricken with grief, Lloyd sheds a few tears before he soon used Harumi's words against her again before jumping off and using Mistaké's gift, which was a parachute, he was picked up by his mother, Nya and P.I.X.A.L, all grieving for their "dead" friends.