Events in After Story take place immediately after the first season, following Tomoya's final semester of high school. After declaring his love to Nagisa, they begin to have a close relationship. Their life together will be faced with unexpected challenges, as the truth behind the illusionary world and the city's legend come to light.

Plagued by a seemingly endless stream of haunting dreams, Tomoya drifts through life with an almost overwhelming sense of anger and emptiness. Then, one fateful day, he meets the mysterious and beautiful Nagisa, and his world begins to change. While helping Nagisa revive the defunct Drama Club at their high school, Tomoya discovers that she has the same dreams. Their story starts beneath the cherry blossoms, but where will fate lead them?