Search engine bots don't have javascript, so they won't see any content that was dynamically added to your page via AJAX, etc. In your browser options, turn off Javascript and reload your website. All that they'll see is the content and the links there.
The solution: on your page, in the plain HTML place a link to a page which shows the rest of your content (the stuff that you would load via AJAX), then have Javascript replace that link with the content. The search engine bots will see the link and follow it, indexing all your content. Just make sure that on these lo-fi pages, you provide links back to the regular page, since that's what Google will link to.