Jennifer Keller knows exactly how John Sheppard feels about Rodney McKay, even though he's never admitted to it. She and Rodney have started to see each other, and she's actually taking great pleasure in John's discomfort. However she pushes John too far, and he admits his feelings to Rodney.
When the Expedition travels to Atlantis, the Stargate Shield has been set only to allow Ancients to re-enter the City, only those with the Gene. Sumner and Weir never materialise, and the first person to enter the City with the Gene is Sheppard, others around him aren't being materialised, so John Radios for the SGC to stop sending personnel. Unintentionally, John is able to mentally deactivate the Shield, allowing one other member of the Expedition through, Rodney McKay, but no one else, and the Stargate shuts down. They're alone; and Atlantis' remaining ZPM doesn't have the power to Dial Earth.