The ending of the story is ambiguous, meaning that the author leaves it to the reader to decide if Shawn dies nor not. In the last paragraph of the book, Shawn's father is sitting in the room with him, a pillow on his lap. Shawn feels a seizure coming on, and as he surrenders to it, he wonders, "What will my dad do?" Shawn reflects that whatever happens, it will be all right, and on that note, the story ends.
The author leaves the ending completely open-ended, providing evidence that can be used either way, whether the reader decides that Shawn lives or dies. Shawn's father's words in the minutes leading up to the end show that he is clearly still wrestling with the question of what to do. He says,
"what if you know what I've been thinking of doing, but you can't do anything about it?...What would you tell me to do, Shawn?"
The fact that he is holding a pillow is an ominous sign; a father in a similar situation, Earl Detraux, had smothered his severely handicapped son with a pillow. Shawn notes that his father sounds exhausted; perhaps he has come to the end of his endurance, and is prepared to end it all for his son. It is clear that Shawn's father loves him, and believes that his seizures are very painful for him. Perhaps when that final seizure strikes, he will kill his son to end what he sees as his terrible suffering.
On the other hand, Shawn's father's words show that he is still unsure as to what is the right thing to do, so maybe he does not kill his son at the end of the book. There is a moment where Shawn's and his father's eyes lock, and they
"are somehow together again...in all (Shawn's) life (they) have never been like this before."
It can be argued that perhaps in that moment, father and son experience a connection, and Shawn's father might have seen the life that exists so vibrantly in the damaged body. Perhaps, in the moments before the final seizure, Shawn's silent declaration of love for his father is heard, and his father does not, in fact, kill his son (Chapter 16).