The conflict in Jonathan Livingston Seagull stems from the differing opinions on the purpose of flight held by Jonathan and by the others of the Flock.
As expressed by his father, "This flying business is all very well, but you can't eat a glide, you know. Don't you forget that the reason you fly is to eat." Jonathan tried to adopt this philosophy, but failed. "I don't mind being bone and feathers, mom. I just want to know what I can do in the air and what I can't that's all. I just want to know." As a result of the inability to conform with the behavioral expectations of the Flock, Jonathan is outcast.
Away from the others, Jonathan discovers much about flight and about himself as he flies with and learns from the Chiang, the Elder Gull, Sullivan, and the others who were learning to fly at a different level. The climax of the part of Jonathan's story that is recorded in the book is probably his success at flying with perfect speed.
The trick was to know that his true nature lived, as perfect as an unwritten number, everywhere at once across space and time...Then, one day Jonathan, standing on the shore, closing his eyes, concentrating, all in a flash knew what Chiang had been telling him. "Why, that's true! I am a perfect, unlimited gull!"...He stood alone with the Elder on a totally different seashore
Jonathan reaches a resolution of the conflict that began his life when he returns to the Flock to help those who were facing the struggles he had faced.
For in spite of his lonely past, Jonathan Seagull was born to be an instructor, and his own way of demonstrating love was to give something of the truth that he had seen to a gull who asked only a chance to see truth for himself.
For Jonathan, showing his love of others by teaching them to fly and to understand their truly unlimited nature allowed him to make peace with the divisions of his past and define his life's purpose.
Yes, the resolution is found in the conclusion of the story.
Jonathan faces conflict with the Flock because he wants to fly in a different way and for different reasons than is accepted. Jonathan faces conflict with himself because he doesn't understand the ways in which the Elder Gull, Chiang, teaches him lessons about flying and, more importantly, about understanding and learning and loving. At first, all Jonathan wants to learn is how to fly - fast.
"I want to learn to fly like that," Jonathan said, and a strange light glowed in his eyes. "Tell me what to do." Chiang spoke slowly and watched the younger gull ever so carefully. "To fly as fast as thought, to anywhere that is," he said, "you must begin by knowing that you have already arrived..."
As Jonathan masters higher levels of flight, he faces his conflict with the Flock and comes to understand that he needs to return. He realizes that there may be others who are outcast, as he was, and that he needs to help them learn about flight and about love.
Jonathan Seagull was born to be an instructor, and his own way of demonstrating love was to give something of the thruth that he had seen to a gulll who asked only a chance to see truth for himself.
The resolution of the story is Jonathan's return to the Flock. As Jonathan works with Fletcher and the others, eventually leading them to return to the Flock to help more of the seagulls come to "see the real gull, the good in every one of the, and to help them see it in themselves," the conflict in Jonathan's life is resolved.