With the Merge having put something of a Happy Ending Override for Ninjago after the rather positive ending of Crystallized, the series doesn't hesitates to show the fallout of this catastrophe and how many innocent people and even our heroes are trying to desperately rebuild their lives or cope with what they lost in the process.
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Season 1
- The Merge: Part 1
- The episode begins with Arin practicing fighting moves with his proud parents watching, until the Merge occurs. It was the last time he saw them as in the aftermath, he is unable to find them. Not helping is that not only did he lose his parents, but after being saved by the Ninja, he witnesses them going missing as well, left with nothing but Lloyd's ruined ninja mask.
- The Merge: Part 2
- Crossroads Carnival
- Beyond Madness
- Lloyd, Arin and Sora learning of Kai's supposed fate.
- Writers of Destiny
- Return to Imperium
- The story of Sora's background of living in Imperium, going by her original name, Ana. Learning that Dr. LaRow was using a helpless dragon to power the city and tells her parents about it, and do they do? Nothing, but disown her and express their disappointment to even call her their daughter.
- Mindless Beasts
- I Am the Danger
- The Calm Inside
- The Battle of the Secondary Monastery
- The vision Lloyd gets from Imperium's Source Dragon, which includes a massive graveyard with ninja masks on the tombstones.
- The Temple Of The Dragon Cores
- Gangs Of The Sea
- Wyldly Inappropriate
- After Wyldfyre and Kai manage to fully fix all the damage Wyldfyre had done to the Lava-tides, they immediately "prank" her back by throwing the Dragon Core back into the Pit of No Return, stating she could never change her ways. Poor Wyldfyre actually sounds hurt by this afterwards now that she's been on the receiving end of a cruel "prank".
- The Last Djinn
- While Skybound in the previous series emphasized what would happen if a Djinn seeked out revenge for the destruction of Djinnjago, this episode ends up having a good-hearted Djinn be the Sole Survivor of Djinnjago's destruction, with Arrakore having lost all hope after losing his home.
- They Call It Doom
- Heatwave getting wounded during Kai and Wyldfyre's escape.
- Land Of Lost Things
- The titular Land of Lost Things attracts and imprisons all lost and forgotten things- including people. Cole's gang, the Finders, consists of runaways and outcasts, who are trapped within the realm.
- The Administration
- The last of the lost Ninja, Jay, is revealed to be alive, working for the titular Administration. Surely a reunion is in order- except the other Ninja never encounter him. Worse, if supplementary material is to be believed, Jay has some form of amnesia. Even if they had encountered him, he would have arrested them on the Administration's behalf.
- Absolute Power
- Beatrix's motive to become empress by killing her father by fitting a bomb under his chariot and then pinned the whole thing on her twin sister, next in line, and Elemental Master, Zeatrix.
- We Are All Dragons
- The Power Within
- As Sora is about to step in and fight Beatrix, her parents arrive on the scene. However, to her shock, even after showing evidence of Beatrix's evil, they still follow her. And if that wasn't bad enough, they had the gall to say that Sora abandoned them.
Season 2
- The Blood Moon
- Shattered Dreams
- Beyond the Phantasm Cave
- Force From the East
- The Spell At the Waterfall
- To Mysterium
- Arin's fatal move leaves Egalt half-blind, and a harsh demotion.
- Fugitives From Madness
- Wyldfyre telling Egalt how she lost most of her dragon family to the same disease he has and has made him a stew that'll ease the pain.
- Egalt and Rontu turning to stone when the Blood Moon rises.
- Secrets of the Wyldness
- The Forest of Spirits
- Rising Dragon
- Kai sent to the Nether-Space along with Bonzle.
