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.