Jinta Yadomi and his group of childhood friends have become estranged after a tragic accident split them apart. Now in their high school years, a sudden surprise forces each of them to confront their guilt over what happened that day and come to terms with the ghosts of their past.
The recluse Jintan is stumped when his deceased childhood friend Menma suddenly appears one day and asks him to make her wish come true.
Seeing Poppo at the hideout, Jintan reveals Menma appeared asking him to make her wish come true. Poppo believes Jintan and gives him advice.
Jintan decides to go to school again, thinking that might be Menma’s wish, and also to keep his promise to Anaru.
Yukiatsu tells Jintan and friends he has seen Menma in the woods. Jintan is certain he's lying but goes with the others to find out the truth.
Jintan solves the mystery of the wandering Menma, and confronts the person responsible.
Trying to figure out Menma's wish, Jinta decides to make his long-delayed return to school. However, his return is overshadowed by rumours about Anaru having been spotted at a love hotel.
Anaru has run away from home and is living in the hideout. Jintan tells her she cannot skip school or be away from home forever. Anaru makes a decision.
Jintan has a plan to fulfill Menma's wish, but Menma’s dad is opposed to the idea. Jintan tries to persuade her mom instead.
The gang go round to Jinta's house where they witness Menma's presence first hand, though it is shown that Menma is unable to write anywhere but the secret base. Yukiatsu becomes frustrated that only Jinta can see Menma, whilst Anaru is upset that she can't compare to her.
Jinta asks Menma if she would rather stay here so that they could be together, to which Menma responds that she plans to go on to heaven and be reincarnated.
The gang's cermony to help Menma pass on didn't go as planned, and they realize they need to put their own selfishness aside to figure out what Menma really wants.
