You can create a php or html page that contains the flash intro. Then use .htaccess to load the intro page first. Be sure to redirect to the index page and/or provide a link to the index page.
.htaccess code (if it does not exist, create a new text document and insert the following code, upload it into the main folder of the site and then rename it to .htaccess
RewriteEngine on
Options All -Indexes
DirectoryIndex intro.php index.php index.html index.htm
In this case I used intro.php above. If you want to use an html file, simply rename the intro.php to the name of your web document such as intro.html
(Also the load order above is from left to right. It will first load intro.php if it finds one, if not it will load index.php and so on). The above besides the intro.php is a pretty basic and "default" setup, it should be sufficient. You can also add /noindex.php on the end and create a file called noindex.php in your sites main directory, this way any attempt to browse folders on your site that do not have an index will automatically get thrown to the noindex page.
Example:
RewriteEngine on
Options All -Indexes
DirectoryIndex intro.php index.php index.html index.htm /noindex.php