The series focuses on the main heroine Chiari Tsukikage and her friends on managing the Jewelpet Cafe. One day at the magical world of Jewel Land, Lady Jewelina entrusted Ruby the Magical Jewel Box with a mission to make friends and collect Magic Jewels. At the same time she needs to attend the Jewel Academy to do so and open a shop called the Jewelpet Cafe. However with her friends, things didn't go well as planned with several failed mishaps happened to her and the students being scared, in the point of Ruby giving up. But when she met a young girl named Chiari Tsukikage and decides to help, Ruby's life is about to change forever. Now, she and her friends now must work together for the cafe to prosper, stick together through good and bad luck as well as protecting the Jewel Box from being stolen.

The series is set in the distant future in which the Earth is split in two. The southern hemisphere is placed in another dimension while the inhabitants of the northern hemisphere are able to morph into beast-like humanoids. Eventually the humans of the southern hemisphere, led by Uranus, attack the Beasts. The Three Beasts, Wan Derbard (Wan Dabadadatta) of the Tiger Tribe, Bud Mint (Baado Mint) of the Bird Tribe, and Mei Mer (Mei Mah) of the Mermaid Tribe, are taken prisoner along with Mei Mer's companion Tuttle Millen (Mekka Mannen, also of the Mermaid tribe), but manage to escape thanks to a little girl named Yuuni Charm Password. Together they seek Gaia, which they believe to be a fabulous treasure, but they are pursued by Uranus's minions : V-Darn the vicious mage-knight, V-Sion the warrior woman and Akumako, V-Darn's sadistic imp-like partner.

Following their heroic efforts at Walter Park, the students of the misfit class return to Babyls Demon School after their summer vacation. What awaits them is not only adoration and admiration but also the shocking revelation that, in order to stay in the luxurious Royal One classroom, the entire class must be promoted to Dalet rank before entering the second year. As the Harvest and Music Festivals are right around the corner, there seem to be ample opportunities to rank up. Doing so will not be simple, however, as no class thus far has managed to accomplish such a feat. Hoping to give the misfit class a chance to achieve the improbable, the school appoints special tutors to aid in confronting the challenges that lie ahead. With his sights set beyond Dalet, Iruma Suzuki decides to take strides toward the goal of ranking up, starting with gaining acknowledgement from his special tutor: the short-tempered and selfish Bachiko Barbatos.