It is 1945, Johnny comes home for Christmas, looking older and in good health. He returns again for Spring Break, attends several Broadway shows with his parents, and diverts himself with other cultural entertainment. The family doctor, Traeger, says he's fine, as does his eye doctor, since Johnny had some eyestrain the previous summer. However, he does have a slightly stiff neck.

At school, the doctor there, Johnson, takes Johnny into the infirmary since a stiff neck can indicate polio, although it is unlikely. Johnson brings in Dr. Hahn, a neurologist, to look at Johnny. Hahn calls Gunther and tells him that he thinks Johnny has a brain tumor. After several calls to other doctors, including a specialist in tumors, Tracy Putnam, Gunther and Frances drive to Deerfield. Gunther reflects upon the look on Hahn's face, which was one that knew death was imminent; Gunther identifies, in the unspoken exchange, the knowledge the doctor could not openly communicate. Johnny's right eye also droops.

Gunther learns of the series of events which led to the discovery of the tumor: a nurse was sent into town with Johnny for a metabolism test, and she observed that his eyes were not coordinating properly; she reported this to Johnson, who called in Hahn, who took a spinal tap, which showed pressure in the brain as well as choked optic disks. Gunther remarks on the pain of the spinal tap that Johnny endured and on the other exams he faced for fifteen months. But Johnny never complained, and he was even fascinated by his ailments, asking theoretical questions to his more than thirty doctors. Gunther considers how the doctors, though they loved Johnny—especially Putnam, top in his field and exceptionally selfless and sensitive— did not tell them everything they knew, nor did they know everything.

Johnny is sent by ambulance to Columbia-Presbyterian Hospital in New York. He develops a bad headache, which is fortunately one of the few severe pains of his illness, as the brain itself has no sensory nerves. He manages to stay upbeat and intellectual about his worsening condition. Further tests are performed to try and locate the tumor, but they fail. He has his first operation on April 29, which takes six hours. Traeger has by now explained more about tumors to Gunther: a growth which may or may not be a cancer, a brain tumor does not spread through the body but destroys only the brain by pressure. The pressure can be relieved only by opening the skull. Johnny's tumor is on the right occipital parietal lobe, a difficult spot for extrication.

Putnam's operation removes half of the tumor, which is the size of an orange. Johnny gets somewhat better, but he looks terrible and swollen after a blood transfusion. Revived into consciousness, Johnny says that he could hear the operation going on and asks if there are more tests. He makes a fast recovery, walking within two weeks and exhibiting his normal curious intellect, though he fears blindness and schizophrenia at times. He writes a letter to Albert Einstein about a physics-related idea of his and gets a response. The idea turns out to concern the Unified Field Theory, and a physics professor tells Gunther that he's amazed Johnny is aware of the problem at such a young age. Johnny is seemingly proud of his surgeries and maintains that he feels great, especially to nurses, to whom he is extremely considerate.

Putnam discovers that the tumor is worse than originally thought. Gunther researches tumors and finds out that the kind with the prefix "glio" is always fatal and asks doctors if this is Johnny's type; they assure him that it isn't. Johnny wants only to return to school, but he later criticizes the slowness of Deerfield's curriculum and professes himself ready for Harvard. He writes a prayer, "Unbeliever's Prayer" (also reprinted at the end of the book), in which he apologizes for his agnosticism and thanks God, if he exists, for his life.