The focus of the season is the ninja character Cole as he discovers the dungeons that lie beneath Shintaro Mountain.

The season finale ends with Cole unlocking a new ability that is described as the "Spinjitzu Burst" and defeating the Skull Sorcerer, reavealed to be Shintaro's ruler, King Vangelis.

They discover the Geckles and the Munce, two tribes forced to work in the mines by the evil Skull Sorcerer, but Cole is taken prisoner.

[N 2] Vania leads the ninja to the dungeons, but they are captured by the Awakened Warriors, who can be revived by the sorcerer's Skull of Hazza D'ur.

[N 3] One of the Geckles tells Cole about the Blades of Deliverance, which were wielded by a warrior named "Gilly" who freed the tribes from a dragon called Grief-Bringer.

[N 5] Meanwhile, Kai and Zane are accused by Geckle Chancellor Gulch of working for the Skull Sorcerer and are forced to undergo a "Trial by Mino".

[N 7] After a safe landing at Rock-Bottom, Wu, Cole, and Vania are met by Fungus, Korgran and Plundar who call themselves "The Lowly".

Wu explains to Cole the teaching of the Spinjitzu Burst, who then finds and operates a mech to return the group to the surface.

[N 13] Cole, the Lowly, Princess Vania and Wu discover that the stone-mech is fueled by Elemental Power, and attach it to the mine-carts in an effort to blast their way out of the mountain to confront the evil Skull Sorcerer.

In 2021, Master of the Mountain was nominated for the Leo Awards for Best Direction of an Animated Series for the episode Son of Lilly.