After defeating Empress Beatrix, Lloyd is haunted by visions of a Wolf Clan who has a link to the Blood Moon. Ras and Jordana use the Source Dragon Energy to activate the Shadow Dojo's doors while the Ninja rescue civilians in the city. Arin and Sora are invited by Kreel to the Crossroads where she warns them of a mysterious Night Ghost. They attempt to find the Night Ghost and learn that Lord Ras has returned and plans to complete a blood moon ritual.

Lord Ras and his Wolf Masks arrive at the Cloud Kingdom seeking to obtain dark knowledge. The Ninja learn about the Gong of Shattering from a shopkeeper in the Crossroads. Euphrasia fights against the Wolf Clan but is defeated by Cinder, the Elemental Master of Smoke. Percival rescues Euphrasia after her injury and takes her to the Monastery of Spinjitzu. The Ninja arrive in the Cloud Kingdom and learn about the Forbidden Five and the Blood Moon. Ras uses his new powers against the Ninja. They temporarily retreat at the sight of the power of Shatterspin.

Cinder continues his training on the Shatterspin ability and mocks Jordana. Euphrasia is imprisoned with Vengestone. Back at the Monastery, Nya looks through Master Wu's notes seeking to find information on the Forbidden Five but finds nothing. Lloyd has a vision of the Source Dragons who show him a vision of a mysterious dragon master. Wyldfyre is depressed due to her injury and sneaks on the Destiny's Bounty. The Ninja arrive in the Phantasm Cave where they face their greatest fears. The Ninja escape and find the master they are looking for.

The Finders are ambushed by the Wolf Masks who want to capture Bonzle. The Ninja fight with Egalt but find out it was a test to see if they are worthy. The Dragon Masters, Rontu and Egalt agree to help the Ninja learn the Rising Dragon Technique to stop Shatterspin. The Dragon Masters tell their story of how they defeated the Forbidden Five. Cole arrives in the Land of Lost Things and saves the Finders with the help of a portal gate, but the Wolf Masks have followed them.

Zane and Mr. Frohicky study the portal gate before Cole and the Finders arrive through. The Wolf Masks invade the Monastery of Spinjitzu but are defeated by Zane and Cole, who received help from a mysterious spirit. The Ninja train under the Dragon Masters to learn the Rising Dragon Technique, while Sora and Riyu try to learn Spinjitzu. Wyldfyre is depressed due to her injury and Bonzle tells the story of how she was a spell used to contain the Forbidden Five and defeat them. In a flashback, Bonzle meets Wu and learns she needs a body. Ras speaks to his Master.

Egalt and Rontu oversee ninja training, but Arin's frustration catches Egalt's attention. Meanwhile, Bonzle plans a journey with Cole and Zane to Mysterium. Lloyd encourages Arin to embrace his unique path as a ninja. Egalt's frustration with the ninja's competitiveness leads to a serious injury, resulting in a surprising demotion. Cole, Zane, and Bonzle encounter a villainous puppeteer, Dorama, who traps them in a theatrical scheme until they manage a daring escape, leading them closer to their destination.

In Mysterium, Cole, Zane, and Bonzle meet the Sorceress Gandalaria. Back at the Dragon Palace, Lloyd's visions foretell imminent danger as the Blood Moon rises. Meanwhile, in the depths of the Mysterium Monastery tunnels, Bonzle and Sprite encounter an unexpected adversary: Jay.

Lloyd's visions lead the ninja to the Wyldness where Ras will enact the Ritual of the Blood Moon. Cole, Zane and Bonzle seek protection in Gandalaria's mystical storehouse. Sprite shows Jay a hint towards his past.

In a flashback sequence, young Ras finds himself trapped until he meets his Master. In the present, Ras orders Cinder to destroy the Cloud Kingdom. Meanwhile, the Ninja battle the Wolf Mask Warriors, and Zane, Cole, and Gandalaria must escape the mystical storehouse. Ras's actions set in motion a series of events with dire consequences.

Ras enacts the Ritual of the Blood Moon as he has now captured Bonzle. The Ninja fight against Ras with the help of the Rising Dragon Technique. Ras manages to free one of the Forbidden Five by sacrificing Kai. The portal is closed by the Ninja but Lloyd and Bonzle are trapped. Ras sets a new plan in motion to take over the Tournament of the Sources.