"Himitsu no AiPri" centers on a group of young girls who are chosen to become magical idols, tasked with bringing happiness and hope to people through their performances. The narrative unfolds in a world where negative emotions and despair threaten to overwhelm society. The protagonists, each possessing unique abilities, must balance their ordinary lives with their secret identities as magical idols. Their mission involves battling dark entities born from human sadness and despair, using their magical powers and idol performances to purify these negative energies.

The main characters include Aine, a cheerful and determined girl who becomes the leader of the group; Mion, a calm and analytical member who provides strategic support; and Erika, a passionate and energetic individual who often acts on impulse. Together, they form a cohesive team, learning to harness their powers and grow as individuals while facing various challenges. The series explores themes of friendship, perseverance, and the transformative power of positivity, as the girls work to protect their world and inspire others through their music and performances.

The plot progresses through episodic challenges, with each episode typically featuring a new threat or obstacle that the girls must overcome. As the story develops, deeper layers of the characters' backgrounds and motivations are revealed, adding complexity to their relationships and personal growth. The series also incorporates elements of mystery, as the origins of the dark entities and the true nature of the girls' powers are gradually uncovered. Through their journey, the protagonists not only combat external threats but also confront their own insecurities and fears, ultimately striving to become stronger and more united as a team.