While Lloyd is training his young students Arin and Sora in the Monastery, the Destiny's Bounty appears in the sky and scrapes past the ninja by a hair's breadth. But with a bold leap, the three of them, along with the dragon Riyu, make it onto the ship to look for clues. They dive straight into the Realm of the Madness
The Ninja settle into a new normal after their victory against the Imperium. Lloyd struggles to keep up with the responsibilities of being a Ninja, mentor, and master of the Monastery. They stop another MergeQuake, but the disturbances are getting more frequent. Nya's research guides them to a temple and three Dragon Cores that could stop the quakes for good. Meanwhile, Beatrix plots her revenge and plans to steal the Cores for use as a weapon.
The Ninja split into three teams to find the Dragon Cores that will end the MergeQuakes. Nya pairs with Sora, and Kai ends up with Wyldfyre. Lloyd and Arin head out on the Bounty, but a training mishap crashes them into the sea. To repair the ship, the Ninja must reclaim a floating village from an ocean gang and their monstrous pet crab, but the situation is not what it seems.
Wyldfyre and Kai barely escape another obstacle on their journey. Despite their personality clash, they finally reach the Wyldness. The Dragon Core is possessed by Lava-tides, who force the Ninja to clean up the mess Wyldfyre created when she lived here. Meanwhile, Zane needs a part to study the Monastery's teleportation gate and follows Mr. Frohicky into Crossroads where they are hosting a Zane Day celebration
To locate the yellow Dragon Core, Nya uses a Djinjagan spell that accidentally curses herself and Sora. They become the target of unstoppable spectral Howlers. Sora, the dragon, flies the Ninja to an old ally, Arrakore, the last of the Djinn, but he does not have the magic or the will to help. Back at the Monastery, Mr. Frohicky tries to prove his worth as an Assistant Keeper to Zane, but nothing seems to go right
All three Ninja teams near the end of their hunt for the Dragon Cores. Kai and Wyldfyre scramble for the purple Core against Dorama and the Lava-tides. Lloyd and Arin enter a trial for the pink Core with unexpected consequences. In the Valley of Lost things, Nya and Sora search for the purple Core but instead find an old friend.
Cole reunites with Nya to help her and Sora retrieve the purple Dragon Core in the Land of Lost Things. Unfortunately, the core powers a machine keeping Cole's new home with a group of young runaways safe from a monster hunting the land. Sora studies the machine with the help of a new Elemental Master. Back in the Wyldness, Kai teaches Wyldfyre how to treat Heatwave's burns and hopes the younger fire-user realizes she has more to learn.
Arin and Lloyd follow the stolen pink Dragon Core through a portal into the Administration. The Ninja navigate its maze of cubicles and bureaucracy, inadvertently rescuing Zane along the way. They track down the Core but have to lose an army of Agents if they want to escape. Arin also finds a clue in the continued search for his parents and meets a familiar face in the process. Meanwhile, Kai teaches Wyldfyre the importance of finding calm.
The Empress's rise to power is revealed through flashbacks as present-day Beatrix attempts to construct her new MergeQuake weapon. Deception from a minion delivers her a serious setback. All three teams of Ninja sneak back into the Imperium to retrieve the stolen Dragon Cores. They find help with unexpected allies and form a plan to infiltrate the labs. Unfortunately, they may not reach the Cores before Beatrix completes her weapon.
Life at the Monastery isn’t the same for Wyldfyre since Kai got trapped in the Nether-Space. Her parent-dragon Heatwave knows how to soothe her rage: with a trip back home, to the Wyldness! After all, it’s the perfect place to be angry alone... or is it?
Wyldfyre knows she’s great at lots of things, but babysitting isn’t one of them. Just because she was raised by a dragon doesn’t mean she has any clue how to care for one (or three!). But Kai wouldn’t leave three little dragons to fend for themselves, right?!
Just when Wyldfyre thought things couldn’t get any worse, the baby dragons get lost in a crystal cave. Beautiful as it may be, things aren’t what they seem. With reflections all around, Wyldfyre can’t trust her own eyes and wait… what’s that hissing sound?
There’s light at the end of the cave! If the baby dragons stay calm now, this mission will be accomplished soon. Will Wyldfyre realise that she doesn’t need to do everything alone? It’s time to ask herself, “What would Kai do?”
The Ninja follow a clue to Arin's location but find a new threat, while Nya, Kai and Wyldfyre spark old grudges in their search for Jay.
Arin nurses Ras back to health as they continue his training, meanwhile their trail leads the Ninja into more danger.
Arin ventures into a dangerous new land to heal Ras while Nya and Kai come up with a plan to make Jay come to them.
Zane's search for Arin leads to an old friend but lands him in the middle of the Forbidden Five's hunt for the Prismatic Blades.
The Ninja learn of the Forbidden Five's quest to collect the Prismatic Blades, meanwhile Ras finally leads Arin to his parents.
Sora, Nya and Riyu are summoned to New Djinjago to help a friend, and the mystery bounty hunter receives a new mission.
The mystery bounty hunter tracks Ras and Arin to the World Forest, while the Ninja search for the last Prismatic Blade.
Arin must choose between Ras and the Ninja as the battle for the Prismatic Blades rages across the World Forest.
The Ninja hurry to the First Land to stop the Forbidden Five from freeing ThunderFang, and Wyldfyre discovers a drastic cure to Roby's decay.
ThunderFang is freed, and only the Ninja stand between the Shatter Dragon of Chaos and his revenge.
Ras leads Arin and Sora into unexpected chaos in Mysterium while the Ninja recruit Jay for a special mission.
With Mysterium under attack, Ras, Arin and Sora rely on the Sorceress for help, while Jay leads the Ninja to the Administration on their way to Lee.
Lloyd, Jay, Nya and Wyldfyre go undercover in the strange Land of Lee, while Riyu's training under Rontu is off to a bumpy start.
The Underworld tests Arin and Sora's commitment to Ras, while Nya and Jay work together to expose Lee's secret.
Cole, Frak and Kai unearth a shocking discovery outside the Land of Lost Things, while the Ninja reunite to liberate Lee.
The Ninja escape Lee and head for the source of the threat, while Ras plans his next move.
In the City of Temples, the Ninja find guidance from an unlikely source, while Cole, Kai and Frak battle the Hollow Ones in Imperium.
The Ninja embark on their separate journeys to awaken the Arc Dragon of Focus but deal with unexpected - and annoying - interruptions.
The Ninja reach the Caves of Bells while Lloyd and Arin fight their way through the Spectral Lands to summon the Arc Dragon.
ThunderFang gathers the last of his power in the Spectral Lands and only the Ninja can stop him - but at what cost?