After overcoming the threat of the Easter Corporation, Amu Hinamori and the Seiyo Academy Guardians return to their council duties, eliminating any stray X Eggs they find along the way. With four of the five members graduating this year, the state of next year's Guardians Council is up in the air. In an effort to ensure the council's survival, the group recruits two Guardian Apprentices in the hopes that they will develop their own Heart's Egg someday. One of the Apprentices they take on is Rikka Hiiragi, a spunky and upbeat girl who is capable of communicating with X Eggs. As the Guardians have not been able to speak with these Eggs previously, Rikka's uncanny ability intrigues them. However, Rikka fears that she will never be accepted as a full-fledged Guardian if they ever find out what exactly she does with her ability.

Amu Hinamori and the Seiyo Elementary Guardians continue their quest to seek out and purify X Eggs while in pursuit of the elusive Embryo—an egg said to be able to grant any wish. However, the Guardians must secure the Embryo before it falls into the hands of the nefarious Easter Corporation. As part of their plan to lure out the Embryo, Easter hires Lulu de Morcerf, an aloof girl whose ruby necklace gives her the ability to convert Heart Eggs into Mystery Eggs. These strange Mystery Eggs cannot be purified as easily as X Eggs, and they can force its owner to undergo a Character Transformation. With this growing threat, the Guardians must track down its source and put a stop to them before the matter gets out of hand. Facing insurmountable pressure from these two new objectives, will the Guardians be able to recover the Embryo while also dealing with the Mystery Eggs?

Amu Hinamori is a shy girl who struggles to make friends in part due to the rumors spread around school about her cool and spicy personality. Wishing that she could show everyone her would-be self, Amu wakes up to the presence of three colorful and ornately decorated eggs in her bed. Each of these Hearts Eggs houses a Guardian Character—manifestations of someone's would-be self and their dreams. With the aid of Ran, Miki, and Su, Amu now finds herself able to express who she truly is. However, things do not always pan out in her favor. The sudden appearance of Amu's Guardian Characters prompts the Seiyo Elementary Guardians, a student council-like group with each member possessing their own Guardian Character, to take notice of her. As someone who has multiple Characters, Amu is roped into being the Guardians' Joker, tasked with helping them find X Eggs—corrupted versions of one's Hearts Egg. As she becomes entangled in the Guardians' quest, Amu begins to uncover more about these mysterious Characters, the X Eggs, and the organization that seems to be at the center of it all.