Disclaimer: I don't own Atlantis or these characters, and this story is for fun, not for profit.
A/N: Written in response to a prompt from sg1_five_things.
Four times John almost left Atlantis for good and one time he did
1 – With a new enemy attacking Earth, John was called back to his home world to help in the defense. By the time the defenders had successfully fought off the new threat, and the dust had settled, Earth's resources were so depleted that all missions to the Pegasus galaxy were recalled. That is, until Dr. Rodney McKay, working with his sister Dr. Jeannie Miller, created a prototype energy source dependent on Ancient technology only available in Atlantis. The Atlantis expedition was reconstituted, with Colonel John Sheppard – who had thought he'd said goodbye to that beautiful city for good – as its leader.
2 – Colonel John Sheppard stepped through the Stargate as he'd done hundreds of times before, but at the other end there was no solid ground beneath his feet. Instead he was falling, a chasm having opened just in front of the gate on a planet that he'd visited only once before. Sheppard, plummeting to the ground below, barely had time to register this when his fall was arrested, and he heard a cheerful voice inviting him onto a small ship. Once Sheppard was aboard, the owner of the cheerful voice – and the small ship – gave him a lingering, appreciative glance and introduced himself as Captain Jack Harkness.
3 – It was supposed to be a routine mission: drop off some final supplies and pick up a med team on a sweet little planet with the usual Pegasus woods and villages. But the Wraith were waiting. John Sheppard, refusing repeatedly to give up the codes for Atlantis, was nearly sucked dry when another dart appeared and he was scooped up by the familiar beam. Later, when Todd gave his life back to him and dropped him off near a Stargate on another planet, he almost smiled, "next time we meet, all bets are off."
4 – Chaya visited him in his dreams, not every night, but often enough so that it was impossible to put her out of his mind. Finally, he rose from his bed in the predawn quiet and took the jumper to her planet. She was waiting for him, as he knew she would be. Ever since their first joining he had always known, had always lived with a sense of her presence, her feelings, her longings. Each time they met and shared themselves again, John asked her to let him stay with her. This time he pleaded; he could not live with her constant presence just out of reach. Chaya let him see her love for him one last time, and then released him, sending him back to his own people with nothing more than cherished memories and a free heart and mind.
He had not wanted to be returned to Earth, his flag-draped casket honored by his family's friends – friends who did not know the real John Sheppard. His ashes were scattered in the sea, the sea of the planet where they first found her, Atlantis. Teyla was there with their children. Torren wrapped an arm around his mother's shoulders and held his head high, even while tears streamed down his face. In all those years he had never learned his step-father's way of keeping his emotions inside.