Gwenevere (Starla) is about to follow in the footsteps of her friends Tamara and Fallon as a Jewel Rider: the time has come for her to receive the special Enchanted Jewel, the Sun Stone, in the traditional Friendship Ring ceremony. Gwen's evil aunt, Lady Kale, plans to control Merlin's seven Crown Jewels of the Kingdom that hold powerful magic and rule Avalon forever. Kale finds the mighty Dark Stone and sends Merlin into the hidden realms of Wild Magic. She steals the magical Jewel Box where the Crown Jewels are kept. Kale also captures the winged unicorn named Sunstar, but the Jewel Riders are able to secure the key to the Jewel Box.

Princess Gwenevere and the Jewel Riders, aided by their male counterparts, The Pack, embark on a rescue mission to save Sunstar from Lady Kale's Thornwood Castle. Kale demands the key to the Jewel Box in exchange for the captive unicorn, but Merlin at last moment uses his remaining powers to scatter the Seven Crown Jewels to their original lands and the Jewel Riders manage to set Sunstar free. In order to become a Jewel Rider, Gwenevere enters the revered Circle of Friendship to bond with Sunstar as her magical animal, sharing the Sun Stone with her. But with the Crown Jewels gone from Merlin's Jewel Box, the Wild Magic in Avalon is no longer stable and a great quest to recover the lost Crown Jewels begins.

Tamara is caught in an enchantment when she plays a beautiful harp given to her for a performance at a craft fair. The music of the harp leads Tamara to Rainbow Falls in the Riverdells where the Rainbow Jewel has returned. Gwenevere and Fallon embark on the quest to save Tamara from going into weird trances and to find the Rainbow Jewel before Lady Kale does, and learn what happened to the jewel upon returning to the land.

Trying to ride the Wild Magic by themselves for the first time, Gwen and Sunstar get pulled off course and discover that the Travel Trees, which are used to "ride" the Wild Magic, are being affected as well. It has become very tricky to ride the magic, as they learn when they become separated from the Jewel Riders and must track down the source of a Wild Magic outbreak in the Great Northwoods. The Travel Trees have a crown jewel stuck in their portal and they are disappointed at not being able to dance, so they create a Wild Magic dance floor for all the forest animals. However, Lady Kale has followed them and she steals Gwen's dance partner and captures the Jewel of the Great Northwoods. The Jewel Riders discover that Jewel is being used for evil and fight to reclaim it.

The Jewel Riders and the Pack go on a quest to the Crystal Cliffs to find an ancient mountain called Wizard's Peak and recover the Crown Jewel of Burning Ice. After an ambush by Lady Kale, they separate into two groups; Fallon and the Pack lure Kale away but Gwen and Drake soon find themselves trapped in a labyrinth of ice caverns. Trying to locate the jewel, the Jewel Riders find instead the magical genie Guardian intent on protecting the magical treasures of the ancient Wizards.

A faery, named Wisp, Faery King Odeon's daughter, goes after her lost flock of magic sheep. The sheep became affected by the Wild Magic, turning into "biker-sheeps" through a rainbow passage to the Great Deserts of Avalon. Wisp gets lost following them and needs help to find her way home, when coming across the Travel Trees that took her to Crystal Palace where she meets the Jewel Riders. The Jewel Riders head for the Great Deserts where they discover a secret passage into Faeryland, but Lady Kale has arrived first and decided this is a perfect new kingdom for her to rule. The Jewel Riders, with the help of the Faery Princess, must discover the Desert Star Crown Jewel and save Faeryland from Kale, but the problem is that it is an alternate dimension where magic works differently.

The Pack finds a rhyming entertaining troll in the Misty Moors with the Misty Rose Crown Jewel. The troll uses it to turn the Pack into frogs and their wolves into lizards. Frog Josh escapes and contacts the Jewel Riders who must rescue the boys and recover the jewel. Gwen, Fallon and Tamara must figure out the answers to the riddles of the troll in order to rescue the boys. However a talking swan waddles off with the Misty Rose Crown Jewel, unaware of the Wild Magic havoc it was causing on its trail. The Jewel Riders chase after the swan to recover the jewel and restore the Misty Moors to normal, including the true forms of the troll and swan.

Fallon with Moondance just won a race against the Pack when Tamara informs her that the riders are to go with the princess to a party celerbrating a newborn. Fallon did not wish to leave the Pack's training games for the party that caused a heated argument between her and Gwen. Gwen, Fallon and Tamara must outwit Kale and a band of outlaws as the Jewel Riders escort a trading caravan through a canyon across the Badlands to the party at Castle Greenwood. In the caravan are Fallon’s parents who disapprove of her being a Jewel Rider, leading Fallon to hate Gwen for forcing her to see them again. Later on, when Gwen needs help, Fallon puts aside her anger and saves Gwen. Rescuing Gwen and protecting the caravan, Fallon proves to her parents that she excels as a Jewel Rider and her parents come to accept her choice.

Tamara is called by her parents to Heartland Animal Farm to examine a legendary magical animal recently discovered, a Prism Fox. However, Lady Kale hears the news and now she desires the Prism Fox as one of her magic animals. Using enchanted bagpipes and other instruments, she plays a song to lure away all the animals from the farm, only to discover that her prize is just a baby Prism Fox named Kit. Tamara and friends use their own music and magic to defeat Kale and bring the animals back home. Kit also gets reunited with her parents where they all return home in the Wild Magic.

Drake finds the talking Magic Sword of Garmondale in a tree at a carnival. Hungry for magic from the Enchanted Jewels of the Jewel Riders, the sword promises Drake that women will now fall madly in love with him. With the sword as his love coach, Drake tries some unusual magic love poems out on each of the Jewel Riders. The girls, sensing a trick, turn the tables on Drake by pretending to go along with "his" ruse. As the sword drains away the riders' magic, the girls and Drake outwit the sword, forcing it back to its original state.

Gwen runs off into the Dreamfields of the Great Plains when she becomes bored with her date with Drake. There, she becomes caught in a battle of dreams with Lady Kale who is also trying to find the Crown Jewel. In a wild dream, Kale switches Gwen’s Sun Stone with her Dark Stone and thus a dream world is created in which Gwenevere has become evil, and her aunt has become good. Using the power of the Crown Jewel of the Dreamfields, the two must discover who they really are before it is too late, and Gwen must rely on her friends to help her fight the nightmares of the Dark Stone.

Just when the Jewel Riders try to find the last Crown Jewel and complete the magic of Merlin’s Jewel Box, Lady Kale disguises herself as Queen Anya and sneaks into the Crystal Palace, where she seizes the Jewel Keep and with it the Jewel Box, as well all the magic jewels stored there. Using their powers to create a dangerous "antimagic" device, Kale time-freezes all of New Camelot. When the Jewel Riders find the final Jewel, Kale magically transports it into her hands and strips them of their powers. The girls are helpless to stop Kale from proclaiming herself the new Queen of Avalon.

With Avalon cast in darkness, the Jewel Riders refuse to give up and return to the Friendship Ring to perform the Circle of Friendship ceremony again. Then with their jewels recharged, they enter the Wild Magic to find Merlin, led by their friend Kit the Prism Fox and other special creatures called magic gliders. Merlin reveals that the Crystal Palace itself is an Enchanted Jewel with great powers of goodness, but then Kale also finds him. While he battles Kale in the Wild Magic over the control of the key to the Jewel Box, the girls use Merlin’s Jewel box to release the magic of the Crystal Palace and restore Avalon. Lady Kale is destroyed, but to achieve this, Merlin has sacrificed his magic jewel and he cannot come back.