The book tells the story of Jonathan Livingston Seagull, a seagull who is bored with the daily squabbles over food. Seized by a passion for flight, he pushes himself, learning everything he can about flying, until finally his unwillingness to conform results in his expulsion from his flock. An outcast, he continues to learn, becoming increasingly pleased with his abilities as he leads an idyllic life.
One day, Jonathan is met by two gulls who take him to a "higher plane of existence" (reminiscent of the beliefs of Chinese, in that there is no heaven but a better world found through perfection of knowledge), where he meets other gulls who love to fly. He discovers that his sheer tenacity and desire to learn make him "pretty well a one-in-a-million bird." Jonathan befriends the wisest gull in this new place, named Chiang, who takes him beyond his previous learning, teaching him how to move instantaneously to anywhere else in the Universe. The secret, Chiang says, is to "begin by knowing that you have already arrived...."
Not satisfied with his new life, Jonathan returns to Earth to find others like him, to bring them his learning and to spread his love for flight. His mission is successful, gathering around him others who have been outlawed for not conforming. Ultimately, the very first of his students, Fletcher Lynd Seagull, becomes a teacher in his own right and Jonathan leaves to continue his learning.