When the Ancients returned to Earth, and evacuated the Pegasus Galaxy, they didn't abandon Atlantis, and were able to slip past the Wraith, and fly the City back to Earth. Once they had either Ascended, or Died, Atlantis was left abandoned, and the Second Generation of Humans on Earth, evolved with the City present in their History. Over time, Atlantis was entered, those that didn't possess the Gene could do nothing, but those that did, would use the Atlantis' weapons and defences for their own purposes. It was a point of contention, and cause of many Wars between peoples. Sat smack in the middle of the Atlantic, it has been in dispute for Years, with no one Country allowing another to occupy the City, but it is now under the control of an International Committee, lead by Dr. Elizabeth Weir. Carson Beckett is trying to find people with the Gene, and unexpectedly finds it in a Pilot flying personnel in from the Mainland, Major John Sheppard. Rodney McKay, who has been studying Ancient Technology all of his life, has been brought in from Area 51, and working with Sheppard, is be able to get access to Atlantis' systems. John and Rodney become quite the pair, exploring Atlantis, activating systems, and sometimes spending days entirely alone in the City.