After a mysterious event known as "The Merge" shuffles the universe, an aspiring Ninja teams with a smart techie to navigate a new and unfamiliar world.

Loyd saves Arin and Sora from the Imperium Train and escape with Riyu, who gave them a clue to his home, the Land of the Three Peaks, however Imperium follows them and attempts to capture Riyu's matriarch, and a clash begins.

Lloyd trains Arin and Sora, but they sneak out of the Monastery and go to the Crossroads Carnival, but Lloyd follows them and learns a shocking truth

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

On their way back to Ninjago, our heroes encounter the Monks and browse through their archives, but suddenly a merge-quake occurs and the ninja are in great danger.

Sora tells the other ninjas about her invention: the Photec projection device. But if it falls into the wrong hands, it can wreak havoc. Therefore, Sora and the others decide to return to Imperium to destroy the Photec.

Lloyd encounters a new elemental master while Sora must choose between her past and the future of Ninjago.

To bust the imprisoned dragons out of Imperium, the Ninja will need to work hard, think fast and find one big exit.

Lloyd and Wyldfyre lead the assault on the Claws of Imperium with the freed dragons. Sora and Arin seek out Riyu to defeat the Photacs.

The ninja find allies to free the dragons of Imperium as Lloyd discovers a mysterious energy source beneath the city.

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.

To expose Empress Beatrix's mistreatment of dragons to the naïve citizens of Imperium, the Ninja will need help... from a man on the inside.

Empress Beatrix's rampage pushes the MergeQuakes dangerously close to the tipping point, unless the Ninja can work together — and save the world.