Having grown complacent in the wake of their victory over the Oni, the ninja are enjoying life, playing video-games, sleeping in, and soaking in a hot tub (fashioned from one of the monastery's enormous bells). Unfortunately, this behavior quickly grows tiresome and the ninja are confronted by Master Wu, who accuses them of not taking their duties seriously. The ninja deny this, and Wu decides to put them to the test with a series of booby-traps and pranks intended to test their reflexes and skills. Among the more dangerous challenges, the ninja must catch a dangerous breed of chicken that grows wild in the hills surrounding the monastery. Put to shame by the chicken, the ninja ultimately realize: Wu is right. They have gone soft. They decide to take on a new quest to get back in ninja-shape. 

Realizing they have gone soft, the Ninja search for a quest to reignite their Spinjitzu training and try to cooperate with the police in fighting crime; unfortunately, Ninjago City is enjoying a period of rare tranquility. Having given up hope, the Ninja learn of Clutch Powers' recent discovery and decide to go exploring with him. 

The Ninja set off for their quest in the Desert of Doom, but on the way are attacked by an ancient giant scarab beetle. Eventually, they manage to escape it, but are stranded in the middle of the desert. 

To repair the Land-Bounty, the Ninja must retrieve a critical engine component that has been swallowed by the giant beetle. Zane decides to get swallowed himself, and once he has found the component, the Ninja pull him back up with a rope. Then, they fix the Land-Bounty and escape the beetle. 

The Ninja persuade Clutch Powers to enter the Ancient Pyramid with them and they survive many booby traps along the way. However, they accidentally release Aspheera from her tomb, and she brings the Pyro Vipers to life and entombs the Ninja. She then leads her forces towards Ninjago City, looking for a "treacherous deceiver".

Nelson teams up with Antonia on his first day as a paperboy. While trying to deliver the papers around a rampaged by the Pyro Vipers Ninjago City, they get a message that the Ninja is in trouble. Nelson persuades Antonia to help him warn Master Wu. 

The Ninja are trapped in the pyramid and try to escape, but encounter encroaching lava and traps along the way. They soon understand that their lack of coordination as a team may prove deadly and work together to escape the pyramid. However, when things get very difficult, the Ninja are saved by P.I.X.A.L., who tells them of the Pyro Vipers' attack in Ninjago City. 

While the Pyro Vipers attack Ninjago City, reporters newscast the event which has become known as Snaketastrophy. Meanwhile, Aspheera learns of the Scroll of Forbidden Spinjitzu and sets off for the Ninjago Museum of History, while the Ninja reach the city and battle the Pyro Vipers. 

The Ninja rush to the museum to recover the scroll before it falls into the hands of Aspheera, but they arrive at the same time and battle for the scroll. Its power surpasses Lloyd, but Aspheera acquires the scroll and traps the Ninja. A fan named Jake prompts Kai, now powerless, to never give up and save his friends. 

While Aspheera pursues revenge on the "Treacherous Deceiver" who betrayed her, the Ninja go underground seeking the Serpentine. There, they make a discovery leading them to believe Lord Garmadon is the "Treacherous Deceiver", but Wu corrects them revealing himself to be the one. 

Wu and Lord Garmadon decide to visit the forbidden Serpentine Valley, breaking a peace, and are captured by the Serpentine, but are released by Aspheera with the promise of teaching her the secrets of Spinjitzu. Wu keeps his promise and teaches her, but she uses the power to take over her Tribe. The two brothers use the Scrolls of Forbidden Spinjitzu to overthrow Aspheera, who is entombed for her actions. 

Having learned Master Wu is the "Treacherous Deceiver", the Ninja find themselves under siege at the Monastery, trying to protect Wu from Aspheera. The Pyro Vipers manage to enter the Monastery, but the Ninja, P.I.X.A.L., and Wu have hidden in the underground base. 

The other Ninja learn of the second Scroll of Forbidden Spinjitzu's location from Clutch Powers and break into the Explorer's Club to obtain it, running afoul of the club's manager and irritate club members. In the end, they obtain the scroll but wreak havoc in the club. 

Aspheera breaks into the underground base and confronts Wu, but the Ninja arrive with the second scroll and battle her. Zane eventually defeats her, but she manages to strike him with her scroll. Although the Ninja believe Zane's dead, Wu discovers from Aspheera, who has been imprisoned, that Zane is banished to a distant and remote realm called the Never-Realm. 

Having learned Zane is not dead from Aspheera,but has been banished to the Never Realm, Master Wu prepares to go after him, but the Ninja want to come along as well. When he denies, they take matters into their own hands and defy him. However, Wu uses the Scroll of Forbidden Spinjitzu to stop the Ninja from leaving. However, the Ninja defeat him and go themselves to the Never-Realm, before Wu warns them that there is no way back - the reason it is called the Never Realm. 

The Ninja arrive in the Never-Realm and try to find shelter while wolves attack them, but villagers save them and take them to their village. One of them tells the Ninja about the Ice Emperor and that Zane is in the Emperor's palace. Meanwhile, Vex, the advisor, tells the Emperor that strangers have arrived and prepares to attack the ninja. 

The ninja and the villagers prepare to fight the Blizzard Samurai. While fighting Lloyd and Cole realize that some of them are made of Ice and some were corrupted people. Grimfax extinguishes the Hearth Fire. However, after they defeat the Blizzard Samurai, Kai tries to make fire, using his elemental powers by believing in himself and succeeds in restoring the Hearth Fire, gaining the title "Fire maker". 

The Ninja help the villagers to build weapons in case the Blizzard Samurai return again. Lloyd begins his journey to the Ice castle with the Titan mech tracker that Nya gives him to find it. In his road, he is attacked by wolves, but one of them forces them to retreat. Later, Lloyd gets ambushed by the Blizzard Samurai, but he successfully evades them. He arrives at the Land Bounty, finding it damaged by the freeze.The wolf that forced the others away strangely follows and stays with him. The tracker locates the mech, giving Lloyd hope to find Zane.

When Ultra Violet learns that the Ninja have gone missing, she and The Mechanic plan to escape. In the escape route, they begin to discuss about who is the worst ninja. They are soon interrupted by Fugi-Dove, an infamous criminal. They continue talking along the route. Once they have escaped, P.I.X.A.L catches them and they are thrown back into their cells. 

Back in the Never-Realm, Cole was telling the story of Wu and Zane facing Aspheera. Meanwhile, Lloyd and 'Red' were searching for the Titan Mech. An eagle appears and attacks them. Lloyd and Red enter a cave for safety. They realize that the Titan Mech was held there. Lloyd finds a message from Zane, he repairs the mech, and finally he and Red head out. 

Cole decides to climb a mountain to find a legendary Traveler's Tree where he encounters a Yeti which he has to fight.

Jay and Nya were going up the mountain to go find Cole. Cole ends up in a cave where Krag was. He realizes that the Krag didn't want to hurt him. Krag shows Cole where the Traveler's Tree is and they find it. Jay and Nya meet Cole, who tells them that Krag wanted to help him. 

Lloyd and Red take on their journey to find Zane. Meanwhile, A lightning bolt strikes, unleashing a robot. Red was hurt so Lloyd took her somewhere safe, but when Lloyd wakes up a girl named Akita comes out of nowhere and tries to tell Lloyd she is only a shapeshifter. 

Akita tells her story to Lloyd. Akita and Kataru go alone to get their shapeshifting powers, and they both find them. Meanwhile, Boreal, Vex, and the Ice Emperor freeze the whole village. When Akita and Kataru arrive, Boreal freezes Kataru. 

Boreal strikes again and lays waste to the Ice Fisher's village, forcing the Ninja to go after Lloyd. Lloyd and Akita take on their Journey to find Zane. But they get interrupted by Boreal and Lloyd and Akita fight him. Lloyd is hurt, and they take him to the Ice Palace and show the Ice Emperor, who is revealed to be Zane. 

Back in Ninjago City, Wu and P.I.X.A.L. attempt to locate the Never-Realm and accidentally unleash The Preeminent. Now P.I.X.A.L. has to send her back to the Departed Realm. 

Vex, bitter and seeking revenge from his enemies, meets Zane, who has arrived in the Never-Realm and has lost all of his memories. He tricks Zane into believing he is the Ice Emperor, ruler of the realm with Vex being his trusty advisor. Prompted by Vex, Zane uses the Scroll of Forbidden Spinjitzu to brutally punish Vex's enemies and takes over the Never-Realm, placing it under an eternal winter.

Having discovered the terrible truth of Zane's fate, Lloyd tries to help him remember his true identity, but Vex persuades him into believing Lloyd is a liar. Lloyd is locked up in the dungeons, where he meets Kataru, Akita's brother who has been kept captive for a long time. When all hope seems lost, Grimfax frees them, having believed Lloyd's story and offering to team up with them. Meanwhile, the other Ninja are attacked by wolves, but prevail when they find the Land Bounty and repair it. 

Nya, Jay, Cole, and Kai face off against Boreal, while Lloyd confronts the Ice Emperor himself. Meanwhile, Kataru and Grimfax try to stop the ice army from getting to Lloyd. As Akita wanted revenge, she went to find the ice emperor and tried to kill him. 

Lloyd helps Zane regain his memories. Akita is reunited with Kataru, and the ninja are all reunited. They return to Ninjago city.