[eluser]davidbehler[/eluser]
First you should find out what version of CI you have installed. Easiest way to do this is to go to your system folder/codeigniter/CodeIgniter.php, open it and see what's defined as CI_Version.
Then download a fresh copy of that version of CI, backup your old system folder and replace it with the new one.
Let's just assume they didn't alter any files in the system folder but rather extended the libraries in the application folder. If that's not the case you'll have to copy all the altered files from your backup folder to the new system folder..good luck with finding out which ones were changed
Another step to make debugging easier is to remove the .htaccess file for now and set $config['index_file'] to 'index.php' in application folder/config/config.php. This way you can make sure it's not the htaccess file that causes this.
Another question: Is this a new problem and the site was working before? If so, what did you/the hoster change?