John is in love with Rodney and everyone but Rodney knows, or at least suspects. Everyone respects the pair of them enough to not tell Rodney since they, like John, believe that Rodney is straight. But then a new male arrival to the base takes an interest in the snarky scientist, an interest that Rodney seems to return. Marines and Scientists alike do what they can to discourage John’s competition but Rodney notices and jumps to the wrong conclusion, assuming that they disapprove on moral grounds, leaving him feeling hurt and disappointed. John, meanwhile, is trying to play the supportive friend, but is secretly heartbroken.
Julia Donovan has been granted access to Atlantis, to continue her story for, if and when the existence of the Stargate is made public. She's exploring the city, interviewing personnel, and Sheppard has been assigned to show her around, and demonstrate the gene and its control of ancient technology. John takes her to the labs to meet McKay, and Julia is completely his type, but Rodney's interest isn't stopping her from coming onto John. She's asking them both about their personal lives, noticing the intimacy between them, asking some very awkward questions, and the journalist in her smelling a story, whether there's actually one to tell or not.