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.

block.tpl.php controls how the blocks should be displayed. Div class may be added to the blocks, which helps to let its layout be modified by CSS.