First the file is transformed using the navigation.xsl StyleSheet, performing the following functions specific to the application :

chain	choose the next StyleSheet as specified in layout attribute of the <doc/> tag or the as URL param
map	makes an internal content <map/> using Simple XLinks in the top level of the document
filter	removes unwanted content using the id and to URL params
xlink	dereferences xlink:type="arc" XLinks using the LinkBase to xlink:type="simple" XLinks.
navigation	adds external related navigation <links/> derived from the LinkBase as xlink:type="simple" XLinks to the top level

Next the file is transformed using the hrc.xsl StyleSheet, which lays out the content into HTML.

hrc.xsl imports the shared.xsl performing the following functions specific to the layout's relationship with XLink :

xlink	converting Simple XLinks to HTML
footnotes	displays and builds HTML links to the footnote page
xlink:type="none"	converting application specifc links like <print/> to HTML

This is what the top section of document looks like after processing with the navigation.xsl StyleSheet.

This is what the top section of document looks like after processing with the hrc.xsl StyleSheet.

There is also a StyleSheet for generating XSL:FO for conversion to PDF for print and one for generating QuickTime TextTracks, it's difficult to show you the XML output right now.