Untitled

<!DOCTYPE html>
<html>
<body>
<script>
[...]
// Alerta
alert('Olá!');
[...]
</script>
</body>
</html>

$html = explode(PHP_EOL, file_get_contents('https://example.com/'));
foreach($html as $linha) {
    if(substr($linha, 0, 2) !== '//' && mb_substr($linha, 0, 2) !== '//') {
        $linhas[] = trim($linha);
    }
}
$html = implode(PHP_EOL, $linhas);