The Jewel Riders learn about the newly enhanced magic of their Enchanted Jewels and of a new quest to find the special Wizard Jewels that can give Merlin back his magical powers and return him home. Meanwhile, in the Wild Magic, the ancient wizard Morgana finds her Dark Stone, but realizes that she can not control it because it has been tuned to Lady Kale, who has materialized along with it, so Morgana makes a deal with her to work with her against the Jewel Riders and retrieve the powerful Wizard Jewels. The Jewel Riders return to the Hall of Wizards at the Wizard Peak, where they face Morgana's powers for the first time.

Using maps found in Merlin’s cottage, the Jewel Riders ride the Wild Magic looking for Wizard Jewels. However the Travel Trees cannot handle their new magic and they must travel through the Wild Magic on their own. Tamara finds a place that registers strong magic and the Jewel Riders head there with Magic gliders as their guides. But Morgana has set a trap that send Gwen, Sunstar, Fallon, Moondance and Archie to a place where Morgana can steal the magic of their Enchanted Jewels. Tamara is sent to another place in the Wild Magic where she makes friends with a frightened magical zebracorn named Shadowsong, who was self-conscious about his appearance. Tamara and Shadowsong form a strong bond and must go to the rescue of the other Jewel Riders before Morgana can steal their magic.

It is high fashion and high-jinx as the annual charity fashion show opens at the Crystal Palace fairgrounds. It is Queen Anya’s birthday and King Jared wants to surprise her with a new dress. When he assigns Gwen and Sunstar to handle the “secret mission”, the Princess manages to get Fallon, Moondance, Tamara and Tamara’s baby animals involved in a comedy of errors as each girl and animal tries to complete the mission. Meanwhile, Lady Kale sneaks into the show, creating a style-shifting dress too magical for Gwen to resist. When Gwen puts the dress on, she falls under a spell that the Jewel Riders must break before Gwen leads her evil aunt into the Jewel Keep.

In the magical gardens of Gardenia, a gardener gnome fools the Jewel Riders into thinking that he is one of the Great Wizards from Avalon’s past, and capable of great magic. The gnome has the ability to sculpt magical topiary animals that transform into crystal creatures. When the Jewel Riders discover that the gnome is not what he appears to be (actually just a wizard’s apprentice), they convince the gnome to help them retrieve a powerful Wizard Jewel from a dangerous place called the Sorcerer’s Playground before Lady Kale and Morgana can get it.

The Jewel Riders journey to the enchanted lands of the unicorns to learn about the mysterious secret of their magic. The unicorns, the most magical animals in Avalon, are in danger. The unicorn Queen is missing, kidnapped by Morgana in her quest to obtain the Unicorn Wizard Jewel. Moondance, daughter of the Queen, must go to the magical place and perform a series of tests to determine whether she should become the new unicorn's Queen. This would mean that Moondance can no longer be with the Jewel Riders and leave Fallon. Moondance must choose whether her loyalties are with the unicorns or with her best friend, Fallon.

While searching for wonderous Faery Wraiths in the Forest of Arden, Princess Gwenevere finds romance and magic with a strange boy named Ian. Hearing Gwen’s cry for help, Ian rescues the Princess from a marsh mire. However, the young man does not reveal to the Princess the wondrous magic jewel he has recently found. The jewel has enabled him to transform from a beast to a human boy. Now that he has met Gwen, he is worried that if he gives the jewel away, he will remain a beast forever and lose her love. He must decide what to do because Lady Kale has offered him the chance to remain human forever, if he gives her the magic jewel. When Ian rejects Kale's offer in order to save Gwen, the princess convinces the beast boy that no matter what shape he takes, she will always be his friend.

Gwen and Drake get lost in the misty walls that surround Avalon and discover a new magical but dangerous place outside the borders of the kingdom. Lost, they must work together to unravel a riddle told to them by the Travel Trees. Gwen and Drake must search for a magic wishing jewel that will turn this land to goodness and extend the borders of Avalon before the Wild Magic causes this place to vanish completely. Each discover half of the Wishing Jewel, but they can not figure out why it does not work quite right until they realize that neither of them have the entire jewel so they must work together in order to reassemble its pieces.

A fortune teller named Esmerelda and her mysterious cat use the Fortune Jewel to tell people’s fortunes. When the Jewel Riders have their fortunes read, a dark future is revealed to Gwenevere that tells of the fall of the Crystal Palace and the rise of Morgana to rule Avalon. Gwen and her friends must get this magic jewel to the Jewel Keep and out of Lady Kale's and Morgana’s hands. However, when they fall into a magical trap of Kale, the cat's secret is revealed, being really the ancient wizard Derreck who has lost his human form when he was tricked by Morgana. Will Esmerelda and her cat decide to give the jewel to the Riders, or to Morgana?

Three mischievous trolls find new Enchanted Jewels in the Wild Magic and to energize it, they steal elf magic from the Elf Woods. The Jewel Riders ride into town and look for a Western-style showdown with the trolls to save the elves.

The Wild Magic gliders tell the Jewel Riders a creature is crying from somewhere in the Wild Magic and Tamara convinces the Jewel Riders to go and rescue it. The girls ride into the Wild Magic and discover a “lost island”. But their enemies have also found this island and are looking for magical Wizard Jewel. Morgana sends Kale to follow them. The Jewel Riders find a giant creature who, amazingly, only responds to the baby animals. It is up to Cleo, Sugar and Spike to save the day.

A fortune teller named Esmerelda and her mysterious cat use the Fortune Jewel to tell people’s fortunes. When the Jewel Riders have their fortunes read, a dark future is revealed to Gwenevere that tells of the fall of the Crystal Palace and the rise of Morgana to rule Avalon. Gwen and her friends must get this magic jewel to the Jewel Keep and out of Lady Kale's and Morgana’s hands. However, when they fall into a magical trap of Kale, the cat's secret is revealed, being really the ancient wizard Derreck who has lost his human form when he was tricked by Morgana. Will Esmerelda and her cat decide to give the jewel to the Riders, or to Morgana?

Determined to prevent the prophecy of the Fortune Jewel from coming true, the Jewel Riders travel to the Heart of Avalon to seek out the wisdom of the Lady of the Lake. For this they need the help of the Grandfather Travel Tree, the only one who can send them where they need to go; Lady Kale and Morgana get there first, nearly destroying the tree. Luckily the Riders are able to heal it, and the girls go through its magic tunnel to the shore of the mysterious Isle of Myst, where they are ambushed by Kale and Morgana who turn almost everyone to stone. Only Gwenevere and Sunstar escape across a magical lake, where she is given the magic Staff of Avalon and instructed go to the center of the Wild Magic, where she would merge the Wizard Jewels into a new magical jewel for Merlin. With help by Ian, Gwen triumphs in the final showdown against Kale, who gets herself turned to stone, and restores her friends. But Morgana steals the Wizard Jewels and heads to the center of the Wild Magic first.

Princess Gwenevere and the Jewel Riders journey to the center of the Wild Magic, where they confront Morgana for the control of the magic of Avalon. Morgana is trying to forge the Wizard Jewels together and create the One Jewel that will control all of the wild magic. The final showdown begins as the Jewel Riders battle Morgana in a series of magical events to determine the future of Avalon and the fate of Merlin. The Riders are winning when disaster strikes and Ian sacrifices himself to save Sunstar's life. Can Gwen pull herself together enough to create the One Jewel and save Avalon?