Apparently fanfiction.net has fiddled with their code again, thus making Fanfiction Downloader not work for the site.  Hopefully Raimonds is working on the issue, but since I'm terribly impatient, I went off searching for an alternate program.  Fortunately, I found a *fabulous* one:

Gaffer

I have to admit, I like both the ease of set-up (note: you'll probably want either the SimpleOneFile (black text on white background) or the AllInOne (light text on dark background) template) and the information on the output file (original link!  word count!) a bit better than on Fanfiction Downloader.  Plus, Gregory (Gaffer's creator) is continually updating it, which means that Gaffer works on a lot of popular sites and/or more recent sites (including TTH and Archive of Our Own).  In short, Gaffer is awesome.

The downside apparently is that: "Graffer only works on Windows OS with .NET Framework 3.5 installed."  I have to admit, I'm not 100% sure what the .NET framework is, but the program ran on my computer without me having to change a thing (and a link is provided for you to download .NET if necessary).

ETA: Apparently I neglected to explain what the program actually does:)  Essentially, Gaffer downloads all parts of a story from a given archive and saves them using your preferred template.  SimpleOneFile (which is my favorite) combines all of the chapters into a single file, strips out all of the extraneous nonsense (menus, style sheets, etc), and gives you a file with nothing more than plain HTML and the RTF content of the story.