The story in After follows two main parts. The first part takes place during school days, focusing on a group of students who embark on a hiking trip in the Japanese Alps. However, the protagonist, Yuuichi Takawashi, dies during mountain climbing. Due to his reincarnation process, Yuuichi's memories are replayed. To play these memories, it is necessary to have someone you really want to meet in your heart. Thus, the story flashes back to Yuuichi's high-school days, playing until the day of his accident. The second part begins with Yuuichi waking up in a hospital, but not in his own body – rather, in that of the heroine created in the first part of the story. His soul is possessing this person's body, and he must find a way to communicate with those around him without revealing his true identity.
Gameplay in After is typical of visual novels, where you read through static backgrounds and non-animated characters, making choices that can alter the story's direction. There are also unlockable CG scenes and background music available from a gallery.