The following links might help clear up some stuff.
First, the creator's deviantart page.
http://undyingnephalim.deviantart.com/ Then, the subforum for the mod on Total War Center.
http://www.twcenter.net/forums/forumdisplay.php?f=1894 Regardless, let me elaborate.
The game takes place in an alternate version of the timeline present in UndyingNephalim's rather extensive fan Manga.
What kicks off this game is Link putting the Master Sword back, thus sending him back in time... and by extension ripping the timeline a new one.
Link is supposed to end up joining one of the strongest factions, most likely the strongest one opposing Majora.
Majora is the overall antagonist of campaign. His religion spreads much more quickly than a similar religion. If Majora worship hits 50% two factions enter the fight-The Church of Majora and The Ooccaa. Factions that have fallen to Majora worship will work for majora and TCoM will be able to create some of their units. Link and the Ooccaa are the strongest opponents of Majora.
The only 3 factions which, by default, worship Majora are the Twili and Kingdom of Ikana-and neither begins on the map. Beyond that, the Chuch of Majora cannot spawn without them.
The Campaign is very incomplete, but there. All factions are set-there is a hard limit on factions and buildings. Most are major, a few are minor. Of the major ones, ALMOST all are playable. Mercs are in the early stages of implementation. There are still early factions missing units that have yet to be implemented.
Much of this need to be worked on before it is in the campaign-but that's a fraction of the plan. You can glean more info by just using the forum.