The Scarlet Ibis is the story of a young boy whose brother, nicknamed Doodle, is born weak and sickly. The elder of the two, hardy and tough, attempts to mold Doodle into someone capable of surviving in the harsh world of the schoolyard. The eponymous Ibis arrives in their yard one day, beautiful but spent after a storm, and dies of exhaustion. Doodle soon dies as well after the narrator pushes him too hard during a rowing expedition. His death mirror's the ibis's.
The Narrator, who is not named but simply called "Brother", recounts the life of his younger brother, William Armstrong, nicknamed "Doodle". Doodle is born a sickly child who is not expected to live because of his birth defects. His family even has a small coffin made in the case of his death. Doodle survives, but for most of his babyhood, he is unable to move or respond to his environment. Brother even goes so far as planning to smother the baby with a pillow, thinking that having no brother was better than having a brother who wasn't truly there. Luckily, Doodle smiles at Brother before he can do the deed, and, overjoyed, Brother leaves him be.
Doodle eventually learns to crawl, even though the doctor says the strain of even sitting up might kill him because of his weak heart. He crawls backwards, though, reminding the narrator of a doodlebug, leading him to nickname William, "Doodle". But Doodle is still very weak and feeble. Doodle's brother wanted someone who could run and jump and play with him, but resents having the weak and fragile Doodle instead. The narrator even has to pull his brother around in a wooden go-cart his father built him, because Doodle can't walk. It is now that Brother decides to train Doodle to be a "normal human being". He takes Doodle down to the swamp to teach him how to walk.
Eventually, shortly before his sixth birthday, Doodle learns to walk with help from Brother. Encouraged by this, Brother decides to teach Doodle how to run, climb vines, swim, row and even fight to prepare Doodle for school. However, almost a year after the plan was made, Doodle was far from accomplishing the goals by the nearing deadline.
One day, a big red bird appears in their garden, looking sick and tired. The boys' father identifies it as a scarlet ibis, a tropical bird that was blown off-course by a recent storm. When the bird dies, Doodle, pitying the creature, buries it, while the rest of the family looks on and laughs. Afterwards, the boys go to the nearby Horsehead Landing to continue Doodle's "training". On their way back to the house, Brother has Doodle practice rowing. A sudden rainstorm comes, and when they reach the riverbank, Doodle is tired and frightened. Brother, angry and frustrated that Doodle could not finish his training before school starts, runs ahead of Doodle, leaving the frightened boy behind. When Brother does not see Doodle, he returns for him, his anger dissipated. To his horror, he finds Doodle, lifeless, lying on the ground with blood flowing out of his mouth, staining his throat and shirt a brilliant red. Doodle died like the scarlet ibis: bloody red and far away from home.