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.