if I understand you correctly, you want to prevent your cron.php script from getting started a second time by cron, it is not called from another PHP script? (in that case, require_once would be the right answer)
as I understand it, you need to store a marker that indicates that your script is running and remove that marker at the end of your script.
depending on your environment, you could either create a small file, i.e. .lock
or store a status = locked entry in your database.
edit: here is a small code example using the file method:
<?php
// cron.php
$path = '/path/to/your/data/directory/';
if (file_exists($path . '.lock') {
die('cron.php is already running');
}
// if script reaches this point, it is not locked -> create a lock
file_put_contents($path . '.lock', 'lockfile created at ' . now());
//... your code....
//unlocking
unlink($path . '.lock');
?>