At Gerson's nursing home, Johnny's blood count drops ,and he bruises even more. The doctors predict imminent death, but Johnny feels better within a week. Traeger agrees to continue with Gerson's methods, which include rest, daily enemas, and a salt-free, fat-free diet, all under the theory that the body is self-healing. Johnny uses humor to combat the unappealing practice. He gets much better, and Gunther is confident that he will fully recover. Gerson consults with other doctors who previously thought he was a quack. Frances, though, still searches for a possible miracle cure.

Johnny has a nosebleed, and Gerson permits the use of drugs. Frances keeps Johnny in high spirits, reading to him and bringing gifts. Johnny is also interested in the book Gunther is writing, Inside U.S.A. Frances dances with Johnny to help him practice for the distant senior prom. His vision is further impaired, and he is occasionally "subconsciously hostile" to Gunther for his good health. He believes he is healthier than he really is, but once, after dropping playing cards on the floor, he admits his hand is weak and ineffective.

Gunther describes cancer as a cellular rebellion, and Gerson believes that cancerous cells are the product of an embryonic miscue. Gunther reflects on all the qualities of humanity that originate from the brain, and how Johnny is fighting against the chaos the tumor stirs up in his mind. Johnny gets physically stronger, but his bump worsens and develops a second bump. Mount runs a battery of physical tests on Johnny to gauge his brain damage. Gunther considers how, since the tumor (on the right side of the brain) affects only the left side of Johnny's body, the effects are not as bad as they could be.

But Johnny's body deteriorates, and when Gunther tells him he cannot return to school, he furiously makes up his lost time through tutoring. He writes a letter to his headmaster, asking for a reprieve from his unfinished work. His physics teacher visits him, and Johnny writes another letter to his math teacher, asking to take an important algebra exam. He takes a practice test, against his tutor's advice, and passes it.

Johnny worsens, though his doctors are amazed he is still alive. They fight about whether he should undergo more drainage. Gunther and Frances decide on a compromise, which includes surgery while keeping with the Gerson diet. Johnny heads off to the Neurological hospital for what they think will be a day or two, but it turns out to be five weeks.

Before the operation, the bump opens, and Mount makes a highly successful emergency drainage. Johnny's recovery is strengthened, the bump disappears, and everyone believes he will be back to normal within a year, especially when they find out the pus from his bump was sterile, which indicates that the tumor is dead. Johnny returns home for a day and a half over Christmas, but he has to return Christmas night to the lonely hospital. He returns home on February 6 for the first time since August. Mount proclaims the tumor "quiescent" (inactive).