Woolsey suspects that the good people on Atlantis are hiding something from him. He's right. John, Rodney, Teyla, Ronan and everyone else in the city are hiding John and Rodney's relationship from their new leader using lies, misdirection, acting, and a created crisis. Whacky fun ensues. In the end Woolsey does discover the secret (how is your call).
Must include Woolsey remarking calmly at some point, "Colonel, you're out of uniform." to a naked Sheppard in the gate room.