With the divorce of his parents, seven-year-old Koyomi Hidaka makes the important decision to live with his father. As a researcher at the Japanese Institute of Virtual Science, Koyomi's father is involved in the investigation of the phenomenon of parallel worlds. Through his father's job, the young boy meets Shiori Satou, the daughter of another divorced researcher. Soon becoming friends, the two spend much of their childhood together.

As Koyomi and Shiori grow closer together over the years, the two intend to marry in the future. However, their plan comes to a halt when their parents decide to marry each other. Now fated to being step-siblings, the two friends refuse to accept their new reality. Using their parents' research, Koyomi and Shiori escape to a parallel world to start their lives anew together, only to face repercussions that will put the very futures they strove for in danger.