There are a few nicely representative lines in this novel which poignantly capture the novel's underlying themes. One of these lines appears at the end of the introductory section, where the adult Gene is standing near the tree by the river.
Nothing endures, not a tree, not love, not even a death by violence.
This sentence reflects the novel's interest in how people and relationships can change very quickly, even the most profound and seemingly permanent. Gene's changing relationship to Finny is the most obvious example of the changes the novel explores, but Brinker and Leper also undergo significant changes as a result of the war's influence. The school also changes from summer to winter in ways that are rather thoroughly described in the book.
Another representative line comes toward the end of A Separate Peace, when Gene shouts at Finny about what Finny would have done if he had been able to enlist.
You'd get things so scrambled up nobody would know who to fight any more.
This line relates to the confusion of friendship that Gene feels toward Finny in the book and helps to underscore the symbolism of the war. The war is a metaphor for life after youth and it is the force which saps the characters of their youth and innocence.
In this novel, however, the real struggle is fought in the hearts of the characters, not on the battlefield.