If the twist is what I said earlier, than there is no "twist." You wake up in the lab, they explain to you where you are, etc. and you have to cooperate for them to extract the memory DNA from your badass ancestor(the dude you play as, who looks just like you in the present). I could get more into it, but I'm not. Yeah, it's not a twist. It's out in the open right when the game starts....even though there may be one you know about at the end of the game. In that case, SHUTUP
Yeah, I had heard about it and figured it'd be the twist, but apparently not. Oh well. It sounds stupid the way I explain it, but it's actually a pretty awesome plot.
I don't find the plot to be that confusing. Then again, if you don't talk to Lucy or read their emails then you're left out on a lot of small things. But it isn't that hard to understand. I'm just about done with the game. It seems pretty short, but once you add in traveling around the kingdom, finding flags, saving people, finding all the high points, etc. it's pretty long. A lot of fun. Definitely one of the best games I've played.
When you get further into the game and figure out what's really going on you'll understand everything. Until then it does seem like a dumb plot. It's pretty solid though.
If you do the bare minimum for each city, meaning you just get all the info. you need to assassinate your target and kill your target, the game goes by really fast. But there's so much to do on the side, which makes it a lot more fun.