The Girl Who Draws on Whales is set in a fantasy world, several centuries after “The Great Flood.” Sister Wangi and younger brother Banyu live in a sea-village. Wangi has a special bond with the Great Whales that visit their sea-village and they allow Wangi to draw on their backs. Sometimes they return with new drawings on them. Wangi believes that there are other sea-villages or island settlements scattered around and that they are sending her messages but, none of the elders listen to her.

One day, a new whale arrives in the village alone, wounded, and dying—this whale has a new drawing on her back that doesn't look like the previous drawings. Inspired by this mystery, Wangi vows to investigate. Although forbidden by her parents and the village elders, Wangi—along with a stowaway, who happens to be her brother Banyu—embark on a wondrous journey to investigate where the drawings are coming from only to find much more than they were expecting.