After being hacked Fatal error: Call to undefined function get_header() in 404.php on line 1

Question

After having timthumb.php exploited.

The site was upgraded to WP 3.5

It was compromised again, (wp-config included encrypted data as well as the functions.php in the wp-include directory.

After reviewing various sites, I opted to remove ALL files (after backing up the site) and reinstall the code to insure no corrupted files, and to remove any unneeded files still lingering from the various theme/plugin/and versions of WordPress updates.

The home page loads, but all links beyond that are unusable, giving this error

Fatal error: Call to undefined function get_header() in ...404.php on line 1. The Header and 404 php files are in the root of the theme's directory, and there is not modification of the code.

I've wiped the site clean twice now, and extracted the 3.5 install and theme back onto the site to ensure correct file placement.

Answer 1

"Generally this happens when someone has mistakenly put index.php from a theme in the WP install folder, where it overwrites the index.php that is the main WordPress file.

Download WordPress again, and take the one file, index.php from its root folder, replacing the file you now have as index.php

It sometimes means someone has loaded an entire theme into the root WP folder."

You might also want to update your permalinks/htaccess if your homepage is working but pages beyond that are not.