right it's been a while since i played so i forgot which route it was (was it return to the mansion after you left?), it's a shame indeed this game is still one of my favouritess on this site.
The route 3 was an alternative path to route 2. In route 2, you come back to the mansion so gramps does not spend 3 days alone with the girls. Basically, you go there to save them. You now enter route 2, which has 2 endings. On one of them, you literally destroy the world after discovering Milli having willingly sex with gramps and enjoying it. In the other, you somehow avoid it and the world remains safe, but gramps will corrupt the priestess too (whose name I don't remember).
Then there was supposed to be a 3rd route. From this point, the rest is speculation: in this route, you actually uncover the secrets of the mansion and the phantom that has been tormenting Ken. I guess the 3rd girl (the tomboyish tanned girl) also would appear, as she didn't show herself during route 2. I don't know what kind of ending would it be though. Judging for what we already had, I guess Milly would be impossible to rescue from gramps, so Ken would turn himself to the tanned girl so he could be comforted, but she would fall too under gramps dick. I don't know what would happen from there...
Damn, I wish the never done route 3 was some kind of happy ending with the tanned girl (since, as stated, Milli is already lost), but knowing how cruel this game was to the main character, there's no way this could have had a happy ending. Not for Ken, at least.