Some of the titles of the links in the navigation might be confusing, though I try not to make it as such. Here's a general rundown of where the links lead:

INFORMATION
Updates - The Updates page(s). Maintained by using a script called CuteNews (current installation: 1.4.6).
Pokedex Entries - Profiles of the character(s) within the story.
Contact - Possible ways to contact the website owner/maintainer.

LIBRARY
Main Story - The bulk of the fanfiction lays within.
Bonus Stories - Anything that doesn't fit within the main story goes here.
Timeline - A generalized timeline to help figure out what happens at major turning points within Tony's timeline.

MULTIMEDIA
Scrapbook - In other words, the picture gallery. Includes requested art, stuff I have done myself and the like.
Soundtrack - Music that seemed to capture points/situations within the story.
Adopted - Miscellaneous things that I've adopted, most with some twist relating to the site's theme.

LINKABLES
Guestbook - I wonder why I even bother having one of these. It never gets signed.
Awards Received - Where all the awards, reviews & contest entries are put.
Fan Listings - Gotta be a fan of certain things, right?
Links In & Out - I'd be lucky glad if someone linked to this site & links to sites that I'm interested in.

Image Links
Four Way Navigation - the Up direction will take you to the top of the page, Down direction to the bottom of the page, Left direction will take you to the previous section (IE: the previous section that comes before Help would be Links Out) and Right direction will take you to the next section (IE: the next section after Scrapbook would be Soundtrack).
Help - Brings you to this page that you're viewing.
Home - Sends you to the main page. Disclaimers are placed there.