"Mitsuboshi Colors" centers on the daily adventures of three young girls—Yui, Sacchan, and Kotoha—who form a group called the Colors. Their self-proclaimed mission is to protect the peace of their town, Ueno, though their activities often revolve around playful antics and imaginative games rather than any real danger. The trio spends their days exploring the town, engaging in lighthearted mischief, and interacting with the local community, including shopkeepers, park-goers, and even a police officer who humorously tolerates their antics.

Yui, the self-appointed leader, is energetic and confident, often coming up with elaborate plans for their "missions." Sacchan, the most mischievous of the group, enjoys teasing others and has a knack for getting into trouble. Kotoha, the youngest and most innocent, often goes along with Yui and Sacchan's schemes, though her naivety sometimes leads to unexpected outcomes. Despite their differences, the three share a strong bond and a shared sense of purpose, even if their "missions" are largely self-invented.

The series lacks a traditional overarching plot, instead focusing on episodic vignettes that highlight the girls' interactions with each other and their surroundings. These vignettes capture the simplicity and charm of childhood, emphasizing themes of friendship, creativity, and the joy of everyday life. The narrative is driven by the girls' boundless energy and their ability to find excitement in the mundane, whether they're pretending to be detectives, staging mock battles, or simply enjoying a day at the park.

While the series is primarily lighthearted, it occasionally touches on moments of introspection, such as when the girls reflect on their friendships or face minor challenges that test their resolve. These moments are handled with a gentle touch, maintaining the overall tone of innocence and optimism. The supporting characters, including the local police officer and various townspeople, add depth to the setting and provide a backdrop for the girls' adventures, often reacting with a mix of amusement and exasperation to their antics.

Overall, "Mitsuboshi Colors" offers a slice-of-life portrayal of childhood, focusing on the imaginative and carefree world of its young protagonists. The series captures the essence of youthful camaraderie and the simple joys of growing up, making it a charming and relatable experience for viewers.