Every Hole is Outlined by John Barnes (Short Story, MOBI format [Kindle Compatible])
In the deep future, a young woman from an oppressive background is adopted onto a relativistic starship, where she rises to be the captain, encounters ghosts, and eventually takes her place in the universe.
I love ghost stories. Not modern romances that have plots that are sort of about ghosts (who resemble vampires that don't bite), not contemporary urban fantasies where ghosts are fedora-wearing detectives or femmes fatales solving the mystery of their own fatalite -- no, I mean real ghost stories, the kind of thing that you hear around a campfire on a cold fall night, that leaves you shivering and terrified in your sleeping bag. The kind of thing you read late at night during a thunderstorm that makes you wonder what will happen when you turn out the light and dive under the covers.
What I love are the sort of supernatural encounter stories like Maria Leach collected to terrorize a whole generation of schoolchildren, stories like the milk bottles on the grave, or "thanks for bringing Sandy home." They don't fit anybody's template for what fiction is supposed to be, nowadays, but they grip the brain like a cold, soggy-fleshed, bony hand stroking your neck at midnight, and grab your attention like that almost-seen almost-face at the window that dares you to look again.
So besides loving those, I'm also a hard science fiction writer, and to let you in on a little secret, we all love relativity, because the time dilation that is found in the Lorentz contractions is such nice, simple, easy to do math. Relativistic starships are the hard-sf writer's friend.
And then every story should have a hard problem, artistically, either something to make the writer sweat or something for the writer to vault over with pretended ease, and in this case it was the idea of writing about the deep future, a time as remote in the future as the Cro-Magnon, Clovis, or Mungo people are in the past.
So it happened this time that I saw a way for ghosts, and relativity, and the deep future to all be in a story together, along with some speculation about what sort of people might be able to live in starships, and here we are. The story was first published in Jim Baen's Universe in 2006, and reprinted in The Year's Best Science Fiction in 2007.