Drupal is driven by templates file. Basically, files ended in *.tpl.php are the template files.
- page.tpl.php
- node.tpl.php
- block.tpl.php
page.tpl.php controls most of the parts. For example, which CSS files are being called. It also determines what items to display (like your mission/ titles/ primary link menu bar)
node.tpl.php controls how the content should be displayed. For example, you don't want to add the comment link for the nodes, you may set it here.