Author Clare Beams transports readers to 1871, in Ashwell, Massachusetts, which is where The Illness Lesson is set. One day in Ashwell, a large flock of big, red birds descends on the home of Samuel and Caroline Hood. The birds' appearance is unexpected and initially quite perplexing to Samuel and Caroline, who can't make heads or tails of what the birds could mean for their future.
After thinking for quite some time, Samuel contends that the birds are an omen. That their appearance means that his business and career as a philosopher will take off once again after his fame had faded. Caroline is skeptical of her father's thoughts, but eventually buys into them after he promises to build a school. At that school, Samuel says, he will guide each student—all women, Samuel eventually decides—as they embark on what he describes as their intellectual awakenings. After all, Samuel loves each of his students and wants to see the best happen for them.
As Caroline realizes how noble her father's intentions and ideas are (even if his plan is full of holes and inconsistencies), she agrees to help him start the school. She loves her father and wants to see him succeed once again, so she happily helps him.
Not long after Caroline and her father open their school, the students begin to experience strange symptoms. Some sleepwalk; others break out into fits, rashes, headaches, and/or exhibit symptoms of Tourette’s. Samuel and Caroline are perplexed by the student's symptoms, so they enlist the help of a local doctor, who they hope can get the school back on track. But the doctor is sadistic and unable to help the two, which forces Caroline to face her father and the other males around her.
After she realizes that the men around her cannot help her, Caroline makes an important decision: she must confront her own past and deal with her traumas. But to deal with her traumas, Caroline must destroy her past and those around her—including her father.
