PHP: give alert popup then redirect the page

Do something like

header("Location: index.php?Message=" . urlencode($Message));

Then on index.php...

if (isset($_GET['Message'])) {
    print $_GET['Message'];
}

In other words, index.php will always check if it's being passed a message in the url. If there is one, display it. Then, just pass the message in the redirect
if you really want to use a modal popup, generate the js...

if (isset($_GET['Message'])) {
    print '<script type="text/javascript">alert("' . $_GET['Message'] . '");</script>';
}