Johnny is discharged from the hospital on June 1, but he continues going every day for x-rays until June 20, when he returns home to Connecticut. Johnny reveals one time how ill he feels. At home, he looks for information on tumors in the encyclopedia, but his parents have hidden the volume, as it reveals that most tumors end with blindness. His physical activity is restricted, but he busies himself with his science workshop in the garage and with visits from friends and relatives, all the while worrying about his financial and emotional expense on others.
Johnny develops papilledema, a protrusion that damages the optic nerve, and, as a result, he loses a great deal of peripheral vision. A doctor looks at Johnny and says he only has a few months left. The bump on his head opens and leaks pus. Everyday thereafter, his head must be dressed and bandaged. His bump bursts open again, and he is taken to Wilder Penfield, a renowned surgeon. Johnny's case is attracting attention, and when he meets Penfield he asks, "Where's Cushing?" referring to the preeminent brain surgeon he will surely meet soon. Penfield tells Gunther that the tumor will kill Johnny and recommends only procedures that can somewhat improve his health for the remainder of his life, although his recommendation of an occipital lobe amputation, unbeknownst to Gunther at the time, causes blindness. Gunther remarks that he heard of stories with patients in Johnny's condition dying like vegetables and that Johnny lived for a year after this and died with dignity.
Gunther and Frances hold out hope that new techniques for dealing with tumors will be discovered. The doctors, however, suggest euthanasia (assisted suicide or terminating the life of someone suffering from an incurable illness), which is an illegal practice but, in their opinion, a merciful one. Frances reads a newspaper article about how an experimental method of intravenous dosages of mustard gas, which is commonly poisonous, can improve tumors. At Memorial Hospital in New York, they find doctors who are willing to give the controversial method a try. The hospital administers its first injection of mustard gas to Johnny, who maintains his usual upbeat demeanor, but he relies heavily on the philosophical and emotional comfort of Frances, with whom he often discusses death.
The mustard gas produces bad side effects—bruising and a lowered white blood count—but it helps Johnny at first. He returns to the country and devotes himself to making up his lost schoolwork and other activities, such as a complicated chemistry experiment, with the help of Mr. Weaver, a neighbor and chemistry teacher at Andover. The experiment works, and Johnny discovers a new property of ammonia. He tells a visiting teacher of his plans for the next school year and of how he'll make up his lost time. On August 31, another leak develops, and his white blood count dangerously falls below 1000.
Gunther learns of Max Gerson, a doctor whose unorthodox methods of treating illnesses are based on a controversial diet. Gunther is skeptical, but he visits Gerson anyway, finding him an impressive, humane figure. With nothing to lose, he and Frances decide to put Johnny on the diet. They tell Johnny who, for the first time, gets upset, nearly crying and fleeing to his room. He apologizes for his outburst the next day. On September 7, they drive to Gerson's nursing home.
A cap is again placed on knowledge in the struggle against death; there are some things Johnny is incapable of understanding (note his request to go rock- climbing, which is out of the question); some things that are hidden from him (the encyclopedia article on tumors and Penfield's recommendation of the amputation that causes blindness); and some that are simply unknown (the myriad questions the doctors are unable to answer). Knowledge can only get one so far in a struggle against death, and courage is required to face the inevitable fate that knowledge cannot help one avoid.
Gunther says he is omitting his and Frances's emotions at this time, which are "terrors and horrors of anguish." These feelings are all onlookers can manage, while Johnny must brave death alone and cannot afford to fall into self-pity or fear. Gunther also says that he cannot answer the philosophical questions about why suffering exists, especially not why it has afflicted Johnny's brain, his most refined part. Johnny professes at one point, in seeming contradiction to his typical optimistic outlook, that the "worst thing is to worry too little" about death. He implies that one must not agonize over these questions, but nearly revel in them, accepting them as a battle. As Gunther points out, he eventually dies with a dignity that overrides his condition, and it is clear that his brave behavior leading up to this—what made his life special—also makes his death special.
Johnny also grows more realistic and even skeptical in this section when he sees that a promised two-day hospital stint will truly be a long-term stay and when he jokes about meeting Cushing, knowing that his case requires drastic measures. His parents try to defy death, using the desperation methods of the mustard gas and Gerson's diet, but Johnny knows he can defeat death by accepting its imminence. Despite his steadfast conviction he will return to school, his remarks that he will be an historic case suggest he knows that death is inevitable. Instead, he applies his energy to things he can solve before death, like the ammonia experiment. Still, his mini-breakdown at hearing of the further treatment, long overdue, shows that he has been privately enduring great stress and misery despite appearances. His recovery the next day, however, suggests that he thinks first of others and how to make them feel better in an effort to make himself feel better.
As a side note, Gunther notes that only Frances spoke with Johnny about death. Perhaps Gunther's silence on the issue is compensated for by his writing Death Be Not Proud which, as he mentioned in the Foreword, is an attempt to share their experience with others.