Lloyd goes on a mission by himself to the museum, then realizes it was a trap set by Morro, a ghost who escaped the Cursed Realm and who possesses him. The other Ninja lose their elemental powers as a result. After possessing Lloyd, Morro dons the Allied Armor and goes to Sensei Wu's tea shop to get the staff that was given to him by the First Spinjitzu Master. The Ninja and Sensei Wu escape on the Destiny's Bounty, but realize they are being followed by Morro, who uses Lloyd's elemental dragon. Wu reveals to the Ninja that Morro was his first student.

As the Ninja escape on the Destiny's Bounty, Morro boards the vessel and tries to get Sensei Wu's staff, but Wu throws his staff overboard and Morro goes after it while the ship crashes. The Ninja then learn that the staff had three clues to where the First Spinjitzu Master's tomb is, and when they realize that a thief called Ronin stole the Scroll of Airjitzu, the first clue, they go to Stiix, a city built on water, to get the scroll from him. On the way there they are attacked by a ghost that Morro summoned with the Allied Armor, but the Ninja defeat him, discovering that water destroys the ghosts. Sensei Wu tells Nya she must train to become the Master of Water. 

The Ninja try to make a bargain for the Scroll Of Airjitzu with Ronin, but the price is too great. They try to earn some money, but their lack of coordination results in utter disaster. Morro steals the scroll in the end, and escapes having learned Airjitsu, but Ronin gives the Ninja weapons which can defeat the ghosts. Meanwhile, Sensei Wu trains Nya to control water, and discovers that her weakness is feeling weak.

While the Ninja have their fears tested in the haunted temple of the evil Sensei Yang, in another attempt to claim the Scroll of Airjitzu, Nya pays Ronin to take her to her Samurai X cave where they encounter Morro and his ghosts who are after Nya's samurai suit. Nya accepts that she is the Master of Water after she makes it rain in the desert while being chased by the ghosts. Meanwhile, the Ninja get the Scroll Of Airjitzu, but while racing out of the temple to escape a curse, they drop it and Cole gets turned into a ghost when he chooses to retrieve the scroll rather than escape.

The Ninja must travel to the Cloud Kingdom for the Sword of Sanctuary, the second clue on Wu's staff. To get there, they must climb the tallest mountain in Ninjago and jump into a cyclone that passes over. While climbing, the Ninja encounter an avalanche, but Cole's new ghost abilities save them. Eventually, they get to the Cloud Kingdom by using Airjitsu successfully and Morro gets there in time to see them leave. Back at the Bounty, Sensei Wu and Nya capture Ghoultar and demand answers.

The Ninja arrive at the Cloud Kingdom, where they begin their search for the Sword of Sanctuary, but are deceived by Fenwick, who has formed an alliance with Morro and has let him into the Kingdom. Wu, Nya, Misako, and Ronin interrogate Ghoultar on the Bounty. Morro manages to obtain the sword, but the Ninja pursue him back through the cyclone and down the mountainside in Ninjago. All Ninja board the Bounty except Kai, who stays behind and takes the Sword of Sanctuary from Morro as Lloyd temporarily regains control of his body. The Ninja fly off into the sunset, ready for the next step of the mission. 

The Ninja now have all the items they need to get to the tomb of the First Spinjitzu Master, but before they can figure out the last clue that leads to the location of the tomb, Ronin steals the Sword of Sanctuary to give it to Morro in exchange for his cursed soul. Morro takes possession of Ronin to trick the Ninja into travelling to the Caves of Despair before trying to bury them alive. The Ninja escape and Ronin tries to repay them by entrusting them with the real location of the tomb, which is under the ocean.

The Ninja reach the underwater tomb with Ronin's vehicle and manage to survive two protection trials, before encountering Morro. Morro gets trapped and the Ninja find the Realm Crystal at the tomb of the First Spinjitzu Master, but Morro arrives and demands the Realm Crystal in exchange for Lloyd. Kai tricks Morro, but when the Ninja rush off to save Lloyd, Morro manages to obtain the Realm Crystal, which he uses to open a portal to the Cursed Realm and escape.

The Ninja go to Stiix to try to stop Morro from unleashing his master, the Preeminent. The Ninja manage to fend off many ghosts, but when Lloyd gets to Morro, the ghost tries to reason with him, using Lloyd's father as an example. Lloyd hesitates, giving time for the Preeminent to be unleashed, while he goes to the Cursed Realm.

The Ninja must protect Stiix from the Preeminent, but the beast is invincible. Meanwhile, Lloyd uses his father's help to get himself out of the Cursed Realm, and fights Morro across multiple realms, including a realm called "Chima", trying to trap him, eventually doing so. The Ninja gets on a boat with the people of Stiix and Nya unlocks her true potential and creates a wave that drowns the Preeminent. Sensei Wu tries to save Morro, but the ghost feels remorseful and willingly drowns and is erased from existence, having given Sensei Wu the Realm Crystal. Using the crystal.
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