Blue Reflection takes place at Hoshinomiya Girls' High School, where players assume the role of student Hinako Shirai. When Hinako's ballet career comes to an end after a tragic accident, she closes her heart off from the rest of the world. However, her life changes when she meets her new best friends, the magical Shijou twins -- Yuzu, who is adored by her classmates for her cheerful and warm personality, and Lime, who is more logical and selfish.

The twin sisters bestow Hinako with the power of a Reflector, a champion who can manipulate a mysterious parallel dimension known as The Common. Hinako can freely move and shape this mystical realm's beauty with her imagination, but she soon understands the very real perils that await her and her friends. As Hinako learns to treasure her companions and creates new bonds with those around her, she gains new strength to help her fight in The Common.