What does Gene learn about himself by the end of the novel?A Separate Peace by John Knowles

After his return to Devon school and his passage through
time in remembrance of his years there, Gene comes to a self-awareness that he did not
possess while a youth.  Like so many, Gene as a youth has externalized the motives and
feelings that he has had, believing instead that Finny was his rival who wished to
prevent him from educational success and be more popular and athletic than he.  In the
end, Gene realizes that Phineas is the only one he has known who possessed no pettiness,
no insecurity:

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All of them, all except Phineas, constructed at
infinite cost to themselves these Maginot Lines [fortifications] against this enemy they
thought they saw across the frontier, this enemy who never attacked that way--if he ever
attacked at all; if he was indeed the
enemy.

While Gene
acknowledges that he has killed his enemy at Devon, Phineas was not really his
enemy.  Wiser, he becomes aware that real enemy has been always within him:  the
"something ignorant in the human heart."  This realization is what gives Gene "a
separate peace," a peace apart from the regret of having lost a true friend because of
his envy and ignorance.