Blue Reflection: Second Light follows Ao Hoshizaki, a girl who attends summer school for supplementary classes and becomes lost in an unknown world. She meets three girls — Kokoro Utsubo, Yuki Kinjou, and Renya Miyauchi — who have lost their memories and live in an isolated school surrounded by water. One day, a path and portal leading to another world appears and the girls decide to go through it. They eventually come across a monster and unlock a power that lets them fight back. In addition, Blue Reflection protagonist Hinako Shirai will appear in the game having also lost her memories.
As the game progress, players can improve the bonds between the girls, providing new events and unlocking new combat powers. Players can also craft items, with the crafting partner affecting the effectiveness and quality of the item. In addition, characters can request additions to the school, which provide new facilities.