Upon downloading Bootstrap 3.x, you'll get bootstrap.css and bootstrap-theme.css (not to mention the minified versions of these files that are also present).
bootstrap.css
bootstrap.css is completely styled and ready to use, if such is your desire. It is perhaps a bit plain but it is ready and it is there.
You do not need to use bootstrap-theme.css if you don't want to and things will be just fine.
bootstrap-theme.css
bootstrap-theme.css is just what the name of the file is trying to suggest: it is a theme for bootstrap that is creatively considered 'THE bootstrap theme'. The name of the file confuses things just a bit since the base bootstrap.css already has styling applied and I, for one, would consider those styles to be the default. But that conclusion is apparently incorrect in light of things said in the Bootstrap documentation's examples section in regard to this bootstrap-theme.css file:
"Load the optional Bootstrap theme for a visually enhanced experience."
The above quote is found here http://getbootstrap.com/getting-started/#examples on a thumbnail that links to this example page http://getbootstrap.com/examples/theme/. The idea is that bootstrap-theme.css is THE bootstrap theme AND it's optional.
Themes at BootSwatch.com
About the themes at BootSwatch.com: These themes are not implemented like bootstrap-theme.css. The BootSwatch themes are modified versions of the original bootstrap.css. So, you should definitely NOT use a theme from BootSwatch AND the bootstrap-theme.css file at the same time.
Custom Theme
About Your Own Custom Theme: You might choose to modify bootstrap-theme.css when creating your own theme. Doing so may make it easier to make styling changes without accidentally breaking any of that built-in Bootstrap goodness.
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