"Fushigiboshi no Futago Hime" centers on the lives of twin princesses, Fine and Rein, who reside in the magical kingdom of Gem Kingdom. The kingdom is composed of seven distinct regions, each representing a different color of the rainbow and governed by a Star Princess. The twins are tasked with maintaining the balance and harmony of their world by protecting the Star Pillar, a mystical structure that sustains the kingdom's light and energy. However, the Star Pillar begins to weaken, threatening the stability of the entire realm.

Fine and Rein embark on a journey to restore the Star Pillar by collecting Star Drops, magical fragments scattered across the kingdom. Each Star Drop is linked to one of the seven regions, and obtaining them requires solving challenges and overcoming obstacles unique to each area. Along the way, the twins encounter various allies and adversaries, including Bright and Glenda, who assist them in their quest, and the enigmatic Dark Power, which seeks to disrupt the balance of the kingdom.

The narrative explores themes of responsibility, unity, and perseverance as Fine and Rein navigate their roles as princesses and protectors of their world. Their contrasting personalities—Fine being more impulsive and adventurous, while Rein is calm and thoughtful—create a dynamic partnership that drives the story forward. The series also delves into the relationships between the twins and the inhabitants of the Gem Kingdom, highlighting the importance of cooperation and understanding in overcoming challenges.

As the twins progress in their mission, they uncover deeper mysteries about the Star Pillar and the origins of the Dark Power. The story builds toward a climactic confrontation where Fine and Rein must use their combined strengths to restore balance to their kingdom and ensure its future. The series balances episodic adventures with an overarching plot, providing a mix of lighthearted moments and dramatic tension as the twins grow into their roles as leaders and guardians.