John Sheppard is flying high; he's just been made a Lt. Colonel in the Air Force, and is deemed important enough to be given assignments at Area 51. It's there that he meets Rodney McKay, and there that he jeopardises his new Rank.
Atlantis is being prepared to leave Earth, the Pegasus Galaxy has been selected as its destination, and the Ancients that have decided to leave, are saying goodbye to those who have decided to stay. John is one of the Alteran's that has decided to go, excited at the prospect of a New Galaxy. During the journey, he meets another Alteran; Rodney. There's something between them from the beginning, something that develops as they finding a planet, and start colonising Pegasus.
John Sheppard has never been more pissed, six weeks Samantha Carter has been in Atlantis, and in that time, Rodney McKay has been following her around like a Puppy. John never sees him, and when he does, he either talks, or daydreams about her. Now John can appreciate that Carter is hot, and smart, and a good person, but he’s still jealous, and is more than a little disturbed by that.