Sora no Manimani revolves around Saku Ōyagi, a bookworm who moves back to the town he lived in as a child after seven years. He had a childhood friend named Mihoshi Akeno who loved astronomy and would always take Saku outside against his will to look at the stars, or do other outdoor activities, whereas Saku would rather have stayed inside with his books.
Saku broke his arm the day he moved away after trying to catch Mihoshi falling out of a tree; Saku resented her for this, and that she never saw him off. However, this was a misunderstanding since he was too stubborn to listen to the whole story (the fall had put her in the hospital so she could not see him off), and later becomes friends with Mihoshi again after they meet attending the same high school. Mihoshi convinces Saku to join the astronomy club she is a member of, despite Saku actually wanting to join literature club instead. Hime Makita, a girl in Saku's class who has a crush on him, also joins the astronomy club.