At the castle, Gawayne invites everyone in the kingdom of Gemina to celebrate his coronation except Arkayna, who is infuriated that her self-centered stepbrother gets to be crowned king, and directs her intense anger and jealously in her Mysticon training.
Back in Drake City, Piper is plagued by her childhood memories of befriending Zarya, and hesitantly joins Emerald and Arkayna on returning to the Cavern of the Cosmos to recover the third fragment of the Codex.
However, when they are attacked by a group of mushroom monsters, Zarya transforms into Mysticon Ranger, helps Malavaron defeat the creatures, and is eventually convinced to rejoin the team.
Back at Spectra Hand's lair, Tazma remains curious as to where the archway leads to and learns that Queen Necrafa is, in fact, alive on the other side of the gate.
While in a midair battle, Princess Arkayna, Piper and Zarya distract Dreadbane and Tazma while Emerald retrieves her medium-sized purple Codex spellbook and pink Unicorn Bracer from the top of the royal castle.
At Dreadbane's lair, Princess Arkayna, Piper and Emerald find the place where Tazma is casting a very strong spell from Zarya's blue Codex spellbook to control the direction of the meteors.
Arkayna is ready to use its vast magical power and high-level spells to save her mother and stepfather from petrification, but Nova Terron stops her, claiming that the Codex must be destroyed.
The Mysticons then help Princess Kelpie and Queen Truefin redecorate and beautify their undersea kingdom of Coral Keep, as their people return home after many years.
To learn more, Malvaron casts a hindsight spell which takes him and the Mysticons back in time one thousand years ago when the original Dragon Mage, Imani Firewing, had defeated the evil Queen of the Undead in one single blast.
Freezing time, they see that Necrafa had lost the four gems in her necklace when Imani blasted her with the mystical Star Dragon bracer, therefore taking her own life in the process.
Using a special chant with a personal object belonging to all of them, Kaos hypnotizes Kitty and her fellow sky pirates into coming back with him to "give them a taste of their own medicine."
Having read the apocalyptic contents of the prophecy, the Mysticons, Nova Terron, and new astromancer Proxima Starfall all race through ancient caverns to recover a spectral dragon egg before Tazma gets her hands on it.
At the Astromancer Academy, Arkayna apologizes for defying Nova Terron and says a heartfelt goodbye to Proxima who is going to remain on the planet of Earth with Yaga; the twin princesses share another sisterly hug and part for the good of all of Gemina, with the promise to see each other again someday.
Nova Terron realizes (and was unaware) that Mrs. Sparklebottom, who was ordered to protect Zarya's true identity, swapped her with another orphaned baby girl, Proxima, who leaves in tears that her entire history had been nothing more than a fabrication.
The Mysticons and Proxima go on an undersea quest to destroy Queen Necrafa's broken mask by hurling it right into the fiery core of the Rift of Ruin; a volcanic trench that is located in the deepest depths of the sea.
Queen Truefin ensures their survival underwater by using her Silver Trident to give the Mysticons mermaid fish tails and octopus tentacles for Proxima, much to her surprise.
Zarya and Piper subdue her and Proxima blasts the young mermaid warrior-princess with an unusually strong energy beam of pure star magic, claiming that she was merely trying to stop her.
Tazma disregards this sentiment and is about to blast her younger brother to nothing, but it interrupted by the arrival of Doug and Choko who use a shrinking potion to enable Malvaron to take her back with them, while the entire lair is being destroyed by a meteor shower created by Nova Terron and his top-level Astromancer students.
Having donned the fragment of Necrafa's mask and allowing its dark power to consume her, Proxima breaks into the Astromancer Academy, where she snatches the powerless Dragon Disk from her old star master, and turns all of the other top Astromancers into her mindless minions: Spectromancers and commands them to kneel before her while she corrupts the Dragon Disk with her greater, darker star magic; turning the ancient artifact from a bright gold to blood-red.
The Mysticons race against the devious Vexicons to retrieve an ancient and immensely powerful scepter that had belonged to a lazy childlike king thousands of years ago, which gives its wielder mind-control over everyone in the realm.
As Emerald and Citrine have a mother-daughter outing, Arkayna, Zarya and Piper try to deal with a maleficent eclipse that strengthens dark creatures and send into a vicious frenzy.
It is then that the eye of Necrafa's mask glows red and Proxima's voice distorts, and demands that Mallory, Kasha and Willa go to find Eartha, as they should never leave a sister behind.
With Tazma's "help", the Mysticons enter the deepest corners of Proxima's subconscious mind to sever the incredibly strong hold the fragment of Necrafa's mask now has over her.
At the same time, the Vexicons have chosen rebellion as the ambitious Mallory covets the dark powers of the ancient Mask, which totally warps her mind and partially alters her looks, to the concern and uncertainty of her three sisters whom she calls "minions."
With a power-mad Mallory now under the dark influence of Queen Necrafa's mask fragment, the Mysticons and the fully reformed Proxima turn to the unlikeliest of allies to put an end to the Vexicons and the Spectral Hand itself once and for all.
Princess Arkayna and Zarya's mother and stepfather are finally fully restored to living flesh and blood at long last, after many months of petrification, by none other than a reformed Dreadbane who sacrifices himself to bring them back.
Queen Goodfey reunites with Princess Arkayna who introduces her to Zarya Moonwolf, the younger twin daughter she never knew she had, which naturally surprises her when the purple-haired, green-eyed girl addresses her as "Mom" and not "Your Highness."
With the greatest evil force known to Planet Gemina finally obliterated since the fall of the original Mysticons one millennia ago, everyone celebrates, with Queen Goodfey apologizing to Princess Arkayna for not taking into account how Zarya being back into her life would affect her eldest twin daughter, and the three embrace loving.
Mallory, Kasha, Willa and a caged Deeva are imprisoned for their crimes against the realm, whereas Eartha fully accepts her good heart and stays with Emerald in Ruddix Hollow, Nova Terron resigns as Star Master of the Astromancer Academy and gives the honor to Proxima Starfall as "Star Mistress" as compensation for his unknowing hand in her life being affected by him fifteen years ago, as he reconciles with his longtime girlfriend/starmate Geraldine.
Queen Goodfey and King Darius resume their royal duties as monarchs of all of Planet Gemina, and the second generation of legendary Mysticons continue their never-ending heroic deeds to further bring peace and justice to the realm aloft with their new dragon mounts.