John Rodgers is in his last year in high school in a small northern California town where the majority of the townspeople work in the lumber industry. As the youngest son of a father who was a champion athlete, John has always felt pressured by him to excel in his sport of choice, distance running. His father also wants him to put aside his interest in biology--ecologists are the enemy since they threaten his livelihood by protesting clearcutting of redwoods. John can do neither.

In the middle of his senior year he learns that his father has leukemia and is losing ground rapidly. Never having had a comfortable relationship with him, the illness complicates their relationship which soon becomes even more complicated by John's discovery of a rare species of butterfly in the company woods. Knowing it will alienate him not only from his father but from the whole town, he reports the discovery and takes the consequences; his friends beat him up and he runs away. With the help of a sympathetic biology teacher he returns home to find his way to a "separate peace" with his father and a new, complex understanding of the trade-offs between loyalty and responsibility.