Peace has returned to Ninjago, and the Ninjas have grown lazy. Rumors of Lord Garmadon's return prompt them to investigate, but they only find his son, Lloyd Montgomery Garmadon, causing mischief.
Driven by a desire to become like his father, Lloyd uncovers the tomb of the Hypnobrai tribe. The tribe's general Slithraa attempts to hypnotize him, but accidentally gives Lloyd control of the tribe. The Ninjas come across the prophecy of the legendary ''Green Ninja'' and, believing one of them is destined to become him, begin fighting amongst themselves, while the Serpentine attack Jumanakai Village.
The Ninja resume their training, preparing for the looming threat of the Serpentine. Lloyd and the Hypnobrai build a treehouse fortress to conquer Ninjago, but it is destroyed by the ninja. When they return to the Monastery of Spinjitzu, they discover that it has been burned down. Zane and the Falcon again, find them a new home – a ship called the ''Destiny's Bounty''.
At the Hypnobrai tomb, Skales takes control of the tribe and banishes Lloyd from the tomb. Seeking revenge, Lloyd uncovers the Fangpyre tomb and m a deal with General Fangtom. Lloyd and the Fangpyre plan to attack the Hypnobrai, but when the two Serpentine generals meet, they become allies and Lloyd escapes. While settling on Destiny's Bounty and preparing it to be their new headquarters, the Ninjas are visited by Jay's parents – Ed and Edna. When the Fangpyre Raid Ed and Edna's junkyard, looking for vehicles to convert into weapons, Jay must rush to save his parents from their transforming venom.
Looking for new allies, Lloyd goes to the Anacondrai tomb and releases Pythor – the last of the Anacondrai Tribe. Pythor initially pretends to be his friend, but eventually betrays him too, stealing his map that shows the locations of the 2 remaining snake tribes. Sensei Wu takes Lloyd under his wing.
Lloyd moves in and plays pranks on the Ninja (including turning Zane's ninja suit pink) to trick them into fighting amongst themselves. Wu encourages him, hoping to teach the Ninja a lesson about unity. Pythor travels to the two remaining Serpentine tombs in an attempt to unite the five tribes, with the ninja in pursuit. Pythor releases the Venomari and Constrictai Tribes from their tombs and plans to unite them under his leadership. When they reach the Venomari tomb, they are surrounded by Serpentine and saved by the mysterious Samurai X. The Ninja infiltrates their meeting and, inspired by Lloyd's pranks, manipulates the tribes into fighting each other. Pythor discovers them, and they are nearly captured, but Zane's pink suit enables them to hide and escape.
Pythor declares himself to be the King of the Serpentine, the destined leader who will reawaken The Great Devourer – an ancient, seemingly immortal beast who will consume all of Ninjago. and begins to search for the lost city of Ouroboros, which is the prison of the legendary serpent. Lloyd, who witnesses all this, is discovered and imprisoned. The Ninja, now wearing new ZX suits, attempt to rescue him, but are nearly captured themselves, only to be saved by the mysterious Samurai X, who Kai discovers to be Nya.
When the four Ninjas follow the mysterious falcon into the woods, they stumble on a hidden workshop where Zane learns the secret about his past; he is a Nindroid, an android made for combat, designed to 'protect those who cannot protect themselves', as said by his deceased father. The discovery of his past allows Zane to unlock his true potential. Meanwhile, Master Wu travels to the realm of madness to find Lord Garmadon.
Jay and Nya have to cut their first date in the Mega-Monster Amusement Park short, as the Serpentine arrives to retrieve the first of the four Fang Blades needed to awaken the Great Devourer. To make matters worse, Jay pricks his hand on the fang of a skeletal Fangpyre, triggering a transformation. The other three ninjas fail to stop Pythor and the Serpentine from retrieving the first Fangblade. Jay unlocks his true potential, saving Nya and overcoming the transformation, while Nya reveals her Samurai X identity. In the Realm of Madness, Wu finds Lord Garmadon, now with four arms, and tells him that Lloyd has been captured.
The four Ninja go undercover as a dance troupe, and enter a talent contest in their quest to win "The Blade Cup", in which one of the Fangblades is hidden, taken from its tomb by Clutch Powers. They ask Cole's father to train them, the leader of one particularly famous dance troupe, the "Royal Blacksmiths", who turns out to be more demanding than Sensei Wu. Lacking confidence in their chances, Cole contemplates stealing the cup but is berated by his father who decides to make him proud by winning the cup. Pythor collapses the stage and steals the cup, while Cole finds his true potential and saves his father. Garmadon returns to Ninjago with Sensei Wu.
The Ninjas are suspicious when Lord Garmadon moves in to help search for his missing son, but realize they have to work together in their attempt to rescue Lloyd from the Serpentine while they dig for the third Fangblade in the heart of the Fire Temple, but are forced to fight the ninja. Lloyd becomes trapped on a rock in the lava, so Kai decides to save him and consequently unlocks his True Potential. On board Destiny's Bounty, the four Golden Weapons reveal that Lloyd is destined to be the Green Ninja. This causes grief to both Wu and Garmadon since their family has now been further divided because the "dark lord" that the Green Ninja has to fight is Lord Garmadon.
At a suggestion from Lloyd to steal back the three Fangblades as Pythor goes for the fourth, the Ninja and Sensei Wu try to infiltrate the inner sanctum of the Serpentine and walk right into a trap. When Lloyd's rescue mission does not go as planned, it is up to Lord Garmadon to save them. Garmadon and the Skulkin Army battle against Pythor and the Serpentine, allowing Lloyd to release the Ninja and get the Fangblades. Garmadon leaves Lloyd to follow his path and the Ninja plan to destroy the Fangblades, but Pythor follows them in secret.
Upon arriving at Torchfire Mountain, the only place where the Fangblades can be destroyed, Pythor reveals himself and steals the blades back, leaving the Ninja to die. Nya saves them, as Samurai X, and they head to the lost City of Ouroboros to try to stop Pythor. After a battle on a Serpentine Truck-fortress, all arrive in the city. Pythor awakens the Great Devourer, but Sensei Wu pins him in place and forces him to watch what he unleashed. Unable to escape, they are both swallowed by the Great Devourer.
The Ninja must fight to save Ninjago. In the end, only Lord Garmadon, using the Four Golden Weapons, can destroy the Great Devourer and manages to kill the snake. Wu is shown to have survived, but Lord Garmadon vanishes with the Weapons and Lloyd must accept the fact that he must face him one day.