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This isn't the detailed description you're after, because I'm working from memory and my Japanese isn't perfect but:

[spoiler]Final final boss is disappointing, nothing much happens beyond some 'oh, well done' messages when you return to town.

'True' ending: you cure the princess of her illness and Fukabito-endowed power, the prince gets his memory back, they live happily ever after without killing each other. The sealed door can be opened and you end up killing the Fukabito thing, who apparently orchestrated this ending and seems happy enough to die at your hand.[/spoiler]

That's probably the least satisfying response I could have written, but by the time I got the 'true' ending I was over-powered, bored and barely reading any more, sorry.

To add on to that,
[spoiler]The English name of the boss is Progenitor, and it's pretty much some bizarre adult version of the Deep One stuck on B10F in the Hall of Conviction. And it's androgynous, too. Just saying.

Anyway, by promising Olympia you won't tell anyone about the City, and by telling Flowdia that it does exist, you get items from both Olympia and Kujura that you can give to the Deep One after reaching the 5th Stratum (the actual route you take up to this point doesn't matter). The Deep One does some crazy shit and you get some key items that you give to the princess and king which leads to what Benkyo described.

Then you get to go the shut-off area of the fourth stratum, and it's all dilapidated and stuff inside. After some super FOE evasion, you reach the Progenitor's boss room and s/he begins talking about how you're going to die...or something. I sort of forget.

The boss itself isn't too bad. The beginning is pretty manageable, but once you get close to beating it, it begins charging elemental power and spamming elemental attacks over and over again so you should have some means of surviving this.

Then, after beating it, you get some funky narrative on how the Deep Ones came down from space and led to the events of EOIII. Also of note is the fact that the Deep Ones are based off of, I believe, Lovecraftian mythology, namely Cthulhu (who's pretty much the postgame final boss).[/spoiler]

...Yeah.