Gunther transcribes the letters Johnny wrote in his life from age seven until near his death. Johnny's early letters display his sensitive, loving side, and his fascination with science and a variety of hobbies that he would take with him throughout his life—music, sports, and sailing. As he gets older, his writing and understanding of the world deepens. In high school, many of his letters report on his academics and activities. After his first operation, he writes a letter to a friend from school to clear up what has happened to him, and he writers several more reports to others. His last letter, to Frances, includes a scribbled note: "Scientists will save us all."
Gunther transcribes a diary Johnny kept over the last few years. Johnny had taken the notebook with him wherever he was while sick. Since Johnny left the diary conspicuously in the open, Gunther and Frances believed he was using it indirectly to communicate to them thoughts he did not want to discuss.
Johnny's early entries, from before he was sick, are brief notes on his life with occasionally introspective notes. One entry lists the five-part "Gunther philosophy," which includes rules and reminders like the Confucian Golden Rule (do unto others as they would do unto you) and "No immortality." His post-tumor entries rarely touch upon his condition, but they continue with philosophical ruminations and directions, academic reports, and day-to-day news. However, on January 8, he writes vulnerably about his fears of death, and as his hospitalizations and restrictions increase, he details his turbulent feelings more ("Oh how tired I feel," April 21st). The last entry, after a list of gifts he meant to give Frances and Gunther, is Johnny's phonetic translation of the Hebrew toast "L'chaim" (he writes "Le Hy-eem"), which means "To Life."
Frances narrates this short section. She brings up all the questions about life that death raises, which she says she discussed with Johnny throughout his illness. To her, he was not merely dying, he was re-born each day. The only answer she can muster to all the philosophical questions is that she wishes they had loved Johnny more. She states that most of the condolence letters they received tried to justify Johnny's death as part of God's mysterious plan. Frances, though a faithful believer in God, does not think God had anything to do with Johnny's illness. In fact, she believes God was as helpless as she was in stopping the tumor. She finds it remarkable that, through his diaries, they were able to see that Johnny knew all along how grave his sickness was despite his constant optimism. The same random fate that produced Johnny and all his remarkable qualities also conspired to produce the tumor.
Frances grieves not out of anger or confusion at God's will, but for the things Johnny loved in which he can longer partake in—sailing, food, science, music. She is happy he was able to graduate with his class. She writes that she no longer fears death, having written over and over to herself instructions to accept it as a "part of Life, like Birth"—except that she accepts it for herself, not for Johnny, who was too young and had too much life in him. She recounts all the activities and passions they shared and feels that their life together was an acknowledged joint "experiment" designed to produce a "newer kind of human being" who was open to all the joys of life. She feels like a guilty failure for surviving her child, and for other things, such as her divorce. She wants to tell other parents to embrace their children, who are alive, not dead like Johnny. She resolves again that the aim of life is to love, to eradicate hate, and that she hopes to love Johnny more and more until she dies, as that kind of love is a "love of love, the love of life."
Johnny's letters provide an opportunity to see the genesis of his personality, especially in his willingness to tinker with things, either physical (note the "bamboo" [sic] flute he crafts) or abstract (his music composition). Later, of course, his science experiments incorporate both sides, but so does his method of dealing with his illness—he alters the state of his physical body through operations and diets as much as he must adjust his mental will. Furthermore, his capacity for love and the potential for that love to show others how to be more loving (what Frances calls the "love of love"), is evident when he stops fishing, thinking about "how I would feel if I were the fish." Frances does not understand at first, but when Johnny shows her, she too empathizes with the plight of the fish.
Johnny's diary is more revealing and, daily reports aside, showcases the high example Johnny set for himself, even before his illness. The "Gunther Philosophy" is one he lived by all along, and the statement "No immortality" is one he always acknowledged but never let defeat him. Johnny may have indeed left his diary out on occasion to communicate to his parents indirectly, but even his rare lamentations—"Oh how tired I feel"—are far from self-pitying. As Frances points out, he soldiered on despite these setbacks and not only for himself, but because he was "bearing out burden"; perhaps Johnny transcribed only his mildly painful thoughts, knowing his parents would read them, and spared them his more fatal ideas.
The diary also records his reading the book Human Destiny, which tries to prove the existence of God through scientific reasoning. While still a staunch atheist, Johnny sees what is worthwhile about religion, especially in its attempts to explain the mysterious. Perhaps he is trying to come to grips with his death, another mystery; in either case, he remains open-minded until the end, willing to explore everything, even that which he steadfastly denies. Frances, on the other hand, tries to understand death through the joy of life and seeks an answer not in religion, but by focusing on Johnny and earthly delights. She feels that her and other people's love for him, and his love for them and for his various pursuits, is what one should remember from a life. Indeed, she seems more aware of the possible joys and loves of life now, so Johnny's life—and death, which she now sees as inseparable from each other—continues in her heart.