First appeared in Fantasy and Science Fiction. Reprinted in Dozois' Year's Best SF. Collected in How We Played the Game in Salt Lake.
A severely ill AIDS patient checks himself into the hospital for pneumonia. His neighbor patient, he's told, is in for a non-contagious pneumonia as well. He's somewhat jealous about the man having family visit as he is alone. However, he overhears the doctors talking about how the neighbor contracted the disease at work, behind several layers of protection. When the neighbor vomits blood, many are exposed. The illness starts to become clearer when they find regular, straight lines in his lungs. It turns out he's been infected by the nano-machines he's been researching. And they will take over the world if allowed to spread.
Spoilers: The neighbor dies but says they can be stopped with radiation. (It's not clear, then, why the X-rays didn't work. Perhaps it's a very specific kind of radiation.) The protagonist volunteers for them to try it on himself first. It works. Salt Lake City is saved. However, an illegal alien working in the hospital and infected has been transported south to Mexico. She deposits nano-mechanisms along the way. The nano-structures are communications equipment pointed at and signaling three different stars. Some suspect evil aliens while the protagonist suspects good, hope for the best. But his guess has no more evidence than those who suspect malevolence. It's not clear why either would be the case except randomness, but it's still cool speculation.
Analysis: The analogous (anything deviating from the norm) can be applied to the protagonist, Maria the illegal alien, AIDS patients and the lonely. Yet these are an integral part of society. The protagonist realizes his dreams by reconnecting with family and with the wife of the researcher--not to mention possibly saving the world. Well worth reading.