The story is about two best friends, Chocolat Meilleure and Vanilla Mieux, who are young witches from the Magical World. They are chosen to compete in a contest to see who can collect the most hearts from human boys. With the help of Rockin' Robin, their mentor and guardian, and two familiars, the competition begins to see who will become the next Queen of the Magical World.
However, trouble begins to brew in the way of the two queen candidates as Pierre, a cold and mysterious boy, begins to win Chocolat's heart and starts to use both her and Vanilla to his own use. Now, both trapped within their own new goals, the two witches must fight their way and retain a friendship which no magic can defeat.
Best friends Mikan and Hotaru grew up in a small town in the remote countryside. When Hotaru moves to a school for geniuses in Tokyo, Mikan misses Hotaru so badly that she decides to travel to Tokyo herself to find Hotaru. She finds Hotaru in a school called "Alice Academy" and finds that the school is actually for people with special powers called "Alices." Narumi-sensei, a teacher at the school, discovers that Mikan also happens to have an Alice, and Mikan is admitted into the academy. At first, she becomes enemies with a boy named Natsume with a fire alice but later Mikan grows to care about him and falls in love with him. She also befriends his best friend, Ruka (or Luca in the English translation). There she finds friends, love, and a life that she will never forget. However, during that time, Mikan and her friends find out that the academy is really built on both secrets and lies.
The heroine of the story, Amu Hinamori, is a student at Seiyo Elementary. At first glance, her classmates refer to her as "cool and spicy" and rumors speculate about her personal life. However, her real personality is that of a very shy girl who has trouble showing her true personality. One night, Amu wishes for the courage to show her "would-be" self, and the next morning finds three brightly colored eggs—red, blue, and green—in her bed. At first, she is alarmed, but realizes she must have really wished to change. These eggs hatch into three Guardian Characters: Ran, Miki, and Su. The Guardian Characters aid Amu in discovering who she truly is and help fulfill Amu's dreams. Amu's life becomes much more complex as she struggles to deal with her "would-be" selves and the Seiyo Elementary's Guardians, who each have a Guardian Character of their own. Later on,they recruit Amu as the "Joker" to search for X Eggs and X Characters, the corrupted forms of people's dreams, so the Guardians can purify their dreams.
Meanwhile, the Easter Company is extracting people's eggs in search of a special egg called the Embryo. The Embryo is believed to grant any wish to the one who possesses it. However, the process creates X Eggs and X Characters. It is described as an all white egg while normal heart's eggs have a yellow heart and yellow wings on it.
Later on in the series, a fourth (yellow) egg named Diamond is born. Unlike Amu's other Guardian Characters, she is only seen a few times in the series. Due to Amu's mixed feelings before Diamond was born, she becomes an X character and is "stolen" by Utau Hoshina, who uses Diamond for her concerts planned by Easter. Later on, Diamond is purified and becomes a regular Guardian Character. She would then would appear in times of heavy crisis.
Lucia, Mermaid Princess of the North Pacific Ocean, sets out to land to find the boy she saved from a shipwreck seven years before the beginning of the story, to whom she had entrusted her pink pearl. She eventually finds the boy: a surfer named Kaito Dōmoto. But as the human form Lucia assumed, named Lucia Nanami, bears very little resemblance to her mermaid form, Kaito cannot recognize her. She cannot tell Kaito who she really is; otherwise, according to mermaid folklore, she would turn into sea-foam. She tries to convince Kaito into figuring out who she really is (since the legend does not say anything about the other person discovering a mermaid's true identity by himself).
At the same time, Lucia has been told that a group of waterdemons or suiyō have invaded the marine world and she must gather the six other Mermaid Princesses and their pearls to bring back the legendary goddess, Aqua Regina, to stop them. To fulfill this, she joins forces with Hanon and Rina, Mermaid Princesses who came up to dry land, use their pearls, turn into singing idols, and use their voices as an offensive power.
