Rodney never falls in love with John Sheppard, the Pegasus galaxy native who'd been shanghaied into becoming their military leader. He's seen that John shoot down pursuing Wraith with such cool efficiency that it was impossible to forget that he'd spent his entire life as a solider in a war his people had eventually lost. It's a frightening thing and, sometimes, it's hard to forget that that look could have just as easily been turned on them if he'd determined the Expedition had been a threat to Atlantis. The Marines, when they see it (or, more specifically, the alien bloodshed that comes with it), immediately decide they like having an Ancient as their commanding officer and adopt him into their military, calling him Major Sheppard and complaining good-naturedly that his skills are wasted as a pilot, even if he is a damned good one.
Major John Sheppard is a hard man. Not cold or cruel or heart-less, as some of the Expedition seems to think, though he creates the persona of being too calm, too cool, too causal to truly care about the lives of the Terran descendants who populate his city. He smiles at them in hallways. He grieves with them when the lives of their colleagues are lost. He appears not to know them as anything more than faces, with names and titles – and, if they're lucky, a skill set or two.
But Major John Sheppard is not a real man.
He knows this. He'd been the one to find him in the first place, bleeding to death in the Control Chair.
Still, its hard to remember that John isn't John, that there is no John, that John's just something an Ancient named Iohannes Ianidedus Licinus Pastor has chosen to answer to, even if it's Iohannes who he watches old SyFy with late into the night, and Iohannes who brings him coffee when he works too long in his lab, and Iohannes he's fallen in love with.