IonCube is installed by default on the servers, however if you require adding custom settings such as increased memory sizes, file upload sizes or change other variables from the default on the server, you will need to create a custom php.ini file for processing. If you use a custom php.ini file on your site, if you do not add in the IonCube references any scripts on your site that require IonCube to work will no longer function. This is true of PDO functionality also.
In order to get it back, you will need to add the following lines to the bottom of your php.ini file:
The above is for PHP 5.3 ONLY. If you are running PHP 5.2, the above numbers must be changed to 5.2 and you can also add in other references for Zend Optimizer. Please see this article on adding IonCube and Zend for a PHP 5.2 site.