The Ninja follow, but are stopped and held up by Nya, who has been polluted with Dark Matter and turned into a slave of the Overlord. In Ninjago, after being discovered, Mystaké reveals her true Oni nature to Garmadon and confronts him, allowing Skylor to borrow his powers and escape, while she is presumably killed. On the Black Bounty, Lord Garmadon is discussing the Mega Weapon with the snake-generals, and he tries to use it to destroy the Ultra Dragon, who happens to be flying by. He attacks it with multiple objects, making the pile grow bigger. While Jay and Nya go out for a date, the other three ninja attempt to stop Pythor and the Serpentine.
They call Sensei and Nya and tell them what happened. In the meantime, Nadakhan finds out what has happened to his crew of , and eventually captures Sensei Wu after accidentally being summoned by him. Once inside, they are met with the Min-Droid. Chen goes after Kai and Nya, Pythor goes after Lloyd, Cryptor goes after Zane, Morro goes after Wu, Kozu goes after Dareth and Samukai is left with fighting Jay. Meanwhile, Pythor has awoken the Venomari and the Constrictai and plans to unite them under him. They explain that these plans include a monstrous weapon known as the Iron Doom, which combines Ray's blacksmithing knowhow with Cyrus Borg's technology and the Time Blades to travel through time, which the Time Twins intend to use to conquer all of time. The Ninja, captured by the Serpentine while trying to rescue Lloyd, are saved by Samurai X, a mysterious warrior who fights against the Serpentine.
Nya then says that if he frees her friends, she'll think about it. Jay tries telling Flintlocke, but Nadakhan thinks he is telling fibs, and the first-mate believes him, so they decided to put Jay in a dangerous game: Scrap 'n' Tap. The Ninja attempt to get Nadakhan out in the open so he'll be exposed to Flintlocke's dart, and eventually they succeed in doing so. All the ninja, joined by Wu and eventually Garmadon, who finally accepted his feelings for his family, form the Tornado, which successfully wipes out all the Oni and turns everyone who was frozen back to normal, thus freeing all the realms from the darkness. Sensei Wu throws his staff off the Bounty and Morro goes to get it.
The Bounty is then struck by a storm and attacked by starteeth, vicious ship-eating creatures that leave the Bounty without any steering, a damaged mast and a hole in their side. Lloyd gets on at the last second and is captured by the Sons of Garmadon, leaving the rest of Ninja to deal with the Sea Monster. Ultra Violet and the Sons of Garmadon attack the royal palace to steal the Mask of Deception. But when Wu chastises the Ninja for their unseemly mirth for their victory over the army, Misako reveals that there might be a way of at least delaying the battle: if the Helmet of Shadows is returned to its pedestal, the countdown might stop. The Ninja succeed in recovering the blade and escaping on the bike and the Ultra Sonic Raider jet, but Machia and the Time Twins are determined to take it back.
Meanwhile, Cole awakens in the middle of the darkness and, upon returning to his Earth Driller, arrives at the Monastery in the middle of the battle and reunites his fellow ninja, who are all happy to have him back. It is then they realize that Harumi is the Quiet One. Lloyd is forced to go on alone as Zane fights the two infected Ninja and Kai fights his still-enslaved sister. With the Anacondrai on the loose, the Ninja visit Ninjago's worst jail. Meanwhile, Garmadon is released onto Ninjago. The Ninja try to get help from Neuro, but he fails to break into Chen's room.
In the meantime, Garmadon goes to steal Baby Wu, but runs into is Misako, Nya and Lloyd. Inside the temple, they find murals depicting all their major victories, and they find a great bell hanging above a strange design on the floor where the Ninjas' symbols reside. While boarding on Chen's ship, they see the other contestants are descendants of the Elemental Masters, guardians of the First Spinjitzu Master, and learn they are not the only ones with elemental power. Meanwhile, the Grundle shows up at the comic shop, but using the illuma-swords and Lloyd´s powers they manage to hold the monster at bay until Sensei and Nya turn up. But it turns out to be a trap, as the boys kidnap the Ninja and try to turn Lloyd back to their side.
The reincarnated Overlord attacks Lloyd, who fights with him and tries to bring back his father. As he summons his power to combat it, he is captured by the Stranger, who reveals himself to be Pythor, having survived being eaten by the Devourer now has his skin bleached white. The Elemental Masters include Skylor, Elemental Master of Amber; Karlof, Elemental Master of Metal; Griffin Turner, Elemental Master of Speed; Paleman, Elemental Master of Light; Tox, Elemental Master of Poison; Ash, Elemental Master of Smoke; Bolobo, Elemental Master of Nature; Gravis, Elemental Master of Gravity; Jacob Pevsner, Elemental Master of Sound; Chamille, Elemental Master of Form; Shade, the Elemental Master of Shadow; and Neuro, Elemental Master of Mind. It is then that Misako tells them of the Temple of Light, where the Golden Weapons were imbued with their powers. Lloyd, Jay, Cole, and Zane head over there while Kai and Nya stay at the bounty to protect Harumi from the Sons of Garmadon.
Lloyd tells Harumi to leave his mother out of their conflict because it was just between them. The djinn says that if she marries him, he'll get infinite wishes. Killow offers Zane Ultra Violet's bike because she has to stay there because the Quiet One who is the leader of the Sons of Garmadon wants them too. Nya and Cole save Lloyd and Misako while Jay, Kai and Zane take on Sons of Garmadon members and try to stop the ceremony. Attempting to ensure their survival, they soon discover that they are not alone, in the realm.
Back at the kingdom, the ninja are deceived by one of the kingdom's headmasters, who has some form of an alliance with Morro and has let him into the Kingdom. The Police Commissioner, the two detectives and Ronin save Nya, Lloyd and Cole from Tiger Widow Island. He tells Garmadon that they need a Super-Weapon unlike anything ever seen. With the arrival of the Ultra-Dragon, the group flies back to Ninjago City and find the city possessed and the Overlord atop a dark tower, morphed into his true Dragon-like form. To prevent good from losing the battle, the First Spinjitzu Master split the land he had created in two, with the Overlord trapped on the dark half of Ninjago, which vanished.