Drupal With CI

[eluser]Unknown[/eluser]
I have what I am assuming is not a unique issue. However, I will rebuild the entire site before I use an iFrame.

I need a xhtml strict compliant way of displaying a CodeIgniter application in a Drupal site. I could build the application in Drupal, but it will be 100 times harder, but at the same time i don't want to build the site in CI for similar reasons.

So I can think of one option. One, I just take the header, footer, and style sheet and build a giant include for my CI app. So they click on the app in the menu, and it looks like they're still in drupal, but it's actually CI.

This is not a very good option, so I'm looking for alternatives. Any ideas?