The Lincoln Train, by Maureen McHugh (Season 2, Episode 3)

A bit of Civil War alternate history, this story won a Hugo Award in 1996 (I said 1995 in the episode, which is the year it was written). It has been released under a Creative Commons, Attribution, Non-Commercial, Share Alike license, along with many of the Maureen McHugh's other works, in a collection called Mothers and Other Monsters. You can find the full text of the story here.

Civil War era music is from History on the Net; the songs were The Vacant Chair and Tramp, Tramp, Tramp. The closing song is Song to the Moon from the opera Rusalka, performed by Zaira Soria, released under a Creative Commons Attribution license.