So, it's not that there's multiple paths through the story.
Instead of routes, think of them as phases.
Right now, we're in the harem phase. Sensei's running around, shagging everything that moves, not terribly concerned with how he might be hurting any of the characters. It's not a true harem (the girls for the most part don't know about each other, most have made it clear they are not okay with sharing, etc), but it almost kinda-sorta feels like one if you skip half the text.
Eventually, this will transition fully into the dark phase. Signs of it have been peeking through since early on, and as it's progressed, the darkness has been more noticeable, but we're not there yet. There are many ways the dark phase could go, it could wind up being very bloody indeed, but it won't be optional. To get to the end, you will HAVE to go through the dark phase, and we'll all be entering it at the same time.
When that phase is over, Sel will begin adding purity routes. Those will be single-girl routes that take them through to their story's conclusion, and will be added individually (order chosen mostly at random, according to the old post on the subject). Once all those are in the game, a final "true" ending will be added.