The story is set up during the two-part pilot episode "Jewel Quest." Princess Gwenevere, the young daughter of the current rulers of Avalon, Queen Anya and King Jared, is being prepared by Merlin for the day when she will meet a bonded animal friend to share their own themed Enchanted Jewels with. Gwen is yet to be given the magic of the royal Sun Stone, while her best friends Tamara and Fallon already wield the magic of the Moon Stone and the Heart Stone. Gwen needs to search for such an animal and become the new leader of the Jewel Riders, and later succeeds in getting her Special Friend in Sunstar the flying unicorn. Meanwhile, the outlaw Lady Kale, a hateful and power-hungry sister of Anya, gets hold of the mysterious Dark Stone and uses it to overpower Merlin, sending him into the perilous dimension of Wild Magic. Kale steals the Crown Jewels and plans to use their magic to take over Avalon and reign forever, but Merlin foils her by breaking their setting and sending them back to the lands from where they had come, scattering them wide across the kingdom and beyond. Unfortunately, once the Crown Jewels' bond is broken, magic is no longer stable and flows out of control, causing dangerous outbreaks until they are brought back together. Retrieving them is the only way the Riders can free Merlin from being lost in the limbo of Wild Magic and so their titular quest begins. Using the magic of the Enchanted Jewels and their friendship, the Jewel Riders must prevent Kale from gaining more power, reclaim the Crown Jewels, and save Merlin and all of Avalon.