John is Ori, and Rodney an Alteran. The Ori despise the Alterans, and they're in the middle of a bitter War, with John and Rodney no being different, they hate each other, but there's something more between them, and although forbidden, they fall in Love. The Alterans are planning to leave the Galaxy, and John must either abandon his people; or Rodney. He leaves with Rodney, joining the Alterans, but he's been bred to despise them, and is distrusted, in case he reveals their New Galaxy's location to the Ori.
Everyone knew that the CIA had tried to recruit Rodney after building a non-working model of a nuclear device in 6th grade, what they didn't know was that he had accepted. He is accepted into a program which trained talented young men and women and upon his 18th birthday is allowed to complete missions. His genius extends to what he learned in the program. He is an expert martial artist, and know everything that a skilled black-ops can do. Eventually Rodney is invited to Atlantis, and although he is retired he is given permission to break cover if the situation requires it. On an offworld mission he runs into a situation that needs his skill. John is in for a surprise, but his surprise is not as great as the others. The real Meredith Rodney McKay appears.
The Ancients left an entire city on Earth, structures and towers covering the entire surface of the planet; that the humans who followed have always lived in. Some humans don't have the gene, others have had it artificially imposed, and time is spent maintaining the City, and continuing the Ancients Research and Experiments. John Sheppard did't grow up in the city, his parents lived on the mainland with the others that wanted a life not ruled by technology, they're not fanatical, but just prefers the mainland. The people who live in the city respect those that live on the mainland, and it's friendly, with people coming and going all the time. John has had a great life so far with his friends Teyla and Ronon, but has always wanted to fly, and seeing the Jumpers flying over head is just too much temptation for him. With the city new to him, he needs some help, and also the go ahead, and training to get his hands on a Jumper. No one is going to just give John a Jumper, and it's going to be tough to find someone willing to give up their time to train him, he never knew it, but John has the gene, and that attracts the attention of Rodney McKay, someone that can make John's dreams of flying, become a reality. Rodney's not a pilot, but is willing to give John his time, if with his gene, John helps him access a lot of the city's systems he hasn't been able to before.
The IOA has pulled the plug, and cancelled the Atlantis expedition. They've decided to abandon the Pegasus Galaxy, and thus eliminate the treat of the Wraith, but they don't plan to abandon Atlantis itself. It's been decided that the city should be brought back to the Milky Way. Teyla and Ronon are furious about that, they see Atlantis as the best hope of defeating the Wraith, and feel that it was left for them, and the people of Pegasus. The IOA has made its decision though; Daedalus won't be making anymore trips, and with Atlantis, goes the only Stargate capable of reaching Earth. The evacuation is slow and steady over the course of several weeks, until only a skeleton crew is left, with McKay and Sheppard left in charge of flying the city home. They have to decide whether to go through with it, and continue on Atlantis in the Milky Way, or essentially steal the city and stay in Pegasus.
When the Shield began to fail, the Expedition evacuated Atlantis before the Failsafe raised the City to the surface, they left before it happened, and not believing it possible to return, never found out. They travelled to another World, and with Teyla and the Athosians, all now essentially Refugees, they set up Camp together. They have nothing, and do try sending Teams through the Gate to gather supplies, and try to find Allies, but they're alone, and don't even know each other. Sheppard and McKay get to know each other.
For a little fun, the Earth side SGC sends Atlantis a special package two weeks before Halloween, a box full of decorations, party supplies and costumes. Any characters, any time frame...have fun!!