Because of his success in teaching Doodle to walk, the narrator decides to teach him other things, too, like running, swimming, climbing trees, and fighting, without telling their parents that he is doing so. Doodle now believes that the narrator is infallible, too, so he goes along with it. They decide that they will complete these tasks within a year, so that Doodle can at last attend school.
Winter does not bring much progress, but when spring comes they start to work harder. They swim and rowboats at a place called Horsehead Landing, and they climb rope vines and have boxing matches in the place where Doodle learned to walk. That summer, in the year 1918, is brutal and rainless; the crops wither and die. Then a hurricane comes, its strong wins yanking up trees. They follow their father out to the cotton fields, where he laments the loss of his crops. Doodle and the narrator, though, take all of this lightly, because they are sure that everything will be all right.
But school is beginning soon, and Doodle is still far behind schedule. They redouble their efforts, and the narrator pushes Doodle extremely hard. He purposely walks fast so that Doodle has to struggle to keep up, and eventually Doodle collapses onto the ground and begins to cry. The narrator asks Doodle if he wants to be different from everyone else when he starts school, and keeps pushing him. Doodle becomes feverish and sick, and is not sleeping well at night. Neither is excited about the training program any longer, but the narrator acknowledges that it is too late to turn back now.
One day when the family is eating lunch and discussing whether or not a storm is coming, Doodle spots a big red bird in the bleeding tree outside. Everyone goes out to see. They observe that it is not frightened of them at all, and it looks tired and sick. Suddenly the bird flies down from the tree, lands at their feet, twitches, and collapses dead on the ground. The family does some research and learns that this is a scarlet ibis, native to places farther south; it must have been swept here in the storm.
Doodle is particularly struck by the death of this bird; he wants to bury him, but their mother refuses, saying it might carry disease. Doodle finds a way to carry it by the neck with a piece of string and buries it anyway, and the family watches from the window while he does. Aunt Nicey pronounces that dead birds are bad luck, particularly red ones.
After this ordeal, the brothers return to Horsehead Landing to practice. Doodle says he's too tired to swim, so they get in a small boat and float off with the tide. Doodle does not speak and keeps his head turned away from the narrator. Eventually the narrator makes Doodle row back against the tide as a storm begins to come in. By the time they reach the shore Doodle is so tired and frightened that he collapses onto the mud. When the narrator helps him up, he smiles up at him in shame, because they both know that Doodle failed at his goals.
They try to race the storm home, but eventually Doodle collapses again. Like he did in an earlier part of the story, Doodle calls out for the narrator not to leave him. The narrator, however, is feeling cruel, since his pride is shattered and they had failed. He runs away, leaving Doodle far behind. He runs for a while and then gets tired, and realizes that what he did was wrong. He waits up for Doodle for a while, but when he does not show, he goes back and finds him in the same spot, lying on the ground, his face buried in his arms.
The narrator lifts Doodle's head and it falls back down, limp; he sees that Doodle had been bleeding from the mouth and is now covered in red. The narrator shakes him and calls his name, but he doesn't move. He observes that Doodle's neck has never looked so long, thin, and fragile. Screaming, the narrator collapses over his brother's body, "sheltering [his] scarlet ibis from the heresy of rain."
This part of the story foreshadows from the very beginning what will happen at the end. The narrator and Doodle face a huge obstacle in the way of their goal when they experience a terrible summer full of droughts, storms, and failed crops. The lost cotton crop that Doodle and the narrator go outside with their father to see represents Doodle himself. The crops were frail and could not survive the stress placed on them throughout the summer, so they wilt and die. Doodle will ultimately do the same, but he and the narrator are not aware of this yet—they still believe everything is going to be all right.
Aside from the effects of the narrator's obvious, destructive pride, this story also has carries an important message about being different, which this section emphasizes more than any other. The purpose of their harsh training regimen is so that Doodle can start school and be just like everyone else. Even though he can walk now, the narrator still insists that this is not enough, and in order to truly blend in with the other kids he must learn to do all these other things. He continuously threatens Doodle and induces in him a fear of being different, but readers must question whether or not conformity truly is necessary or worth it. The tragic outcome of this story confirms that, in this case, it is not.
The narrator briefly mentioned the story's namesake, the scarlet ibis, in the beginning, but it does not come into play again until Part Four. The scarlet ibis is the most prominent symbol in the story, and its death serves as another unheeded warning to the narrator not to push his brother too hard. Aunt Nicey even warns that dead birds bring bad luck, particularly red ones; just like throughout the rest of the story, she serves as the warning voice, always aware and anticipating something the others are not.
By the end of the story, Doodle has become the scarlet ibis. Just like the ibis could not handle the storm to which it was subjected, Doodle was pushed past his limits with the training regimen, ultimately leading to death. Doodle related to the ibis more than anyone else; he felt a connection immediately, which led him to conduct a proper burial for the deceased bird. It is only at the end of the story that the narrator draws this parallel between Doodle and the Ibis, and by then it is far too late.
The color motif is also important to this story. The title, specifying that this ibis is scarlet, tells us that the color red is going to play a major role. The ibis itself is red, and Doodle is covered in red blood when he dies. But red also appears subtly elsewhere; when Doodle is first born in the beginning of the story, his body is described as "red and shriveled." Whenever Doodle faced stress due to physical activity, the narrator emphasized that his face turned red. Over and over again, Doodle is colored similarly to the bird whose fate he will eventually face himself.
Just before Doodle's death, the author infuses the scene with further clues that something bad is going to happen. Often in literature the weather will suit the ensuing events, and in this case, a storm hits as they are practicing rowing out on the river. The narrator suspected the storm was coming, but he still chose to go out with Doodle anyway, once again letting his pride rule his decisions. This storm parallels the one that ruined the cotton crop earlier in the summer.
Another haunting parallel to an earlier part of the story is drawn just before Doodle's death, too. Doodle says, "Don't leave me, brother!" just like he did when the narrator took him to see his casket in the barn. Both times, Doodle was faced with death, the first figurative and the second literal. The difference is the choice the narrator makes in both cases; in the first, the narrator stays. In the second, the narrator's pride once again wins out and he walks away from his ailing brother, and this neglect ultimately leads to Doodle's demise.