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.