A group of six sixth-grade-age childhood friends drift apart after one of them, Meiko "Menma" Honma, dies in an accident. Years after the incident, the leader of the group, Jinta Yadomi, has withdrawn from society, does not attend high school, and lives as a recluse. One summer day, the ghost of an older-looking Menma appears beside him and asks to have a wish granted, reasoning that she cannot pass on into the afterlife until it is fulfilled. At first, he only tries to help her minimally because he thinks he is hallucinating. But 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. All of the group join him, though most of them do so reluctantly.
However, things grow increasingly complicated when his friends accuse him of not being able to get over the death of Menma, for Jinta is the only one who can see Menma's ghost and his friends think he is seeing things. But as matters progress, it is realized that Jinta is not the only person in the group who is having trouble letting go of the past. It is revealed that all of the group members blame themselves for Menma's death and long-hidden feelings are rekindled. The group struggles as they grow from trying to help Menma move on and help each other move on as well.