What’s the basic idea behind PHP files?

Sorry to ask such a dumb question, but I’d like to understand the basic idea behind PHP files. Coming in new to website design a couple of years ago, CSS stylesheets are my natural understanding of how to do it. But now I’m using the Redoable theme which not only comes with a relatively large CSS stylesheet, but also a -lot- of .PHP files.

I understand how CSS styles separate content from format, but what do PHP files do in that same level of operation?

Thanks,

TW