A year has passed since Menma's ghostly return to the Super Peace Busters. Although the time they spent together during that summer was short, the five members reminisce about what happened as they each write a letter to their lost friend.

A group of six childhood friends drift apart after one of them, Meiko "Menma" Honma, dies in an accident. Ten years after the incident, the leader of the group, Jinta Yadomi, has withdrawn from society and lives as a recluse. One summer day, the ghost of an older looking Menma appears before him and asks to have a wish granted, reasoning that she cannot pass on into the afterlife until it is fulfilled. Since Menma does not remember what her wish is, Jinta gathers his estranged friends together once again, believing that they are the key to resolving this problem. However, hidden feelings, internal conflicts, and lingering feelings of bitterness from Menma's parents result in complications for the group as they struggle to help not only Menma move on, but themselves as well.