Sweet! I really liked the twist near the end, where the player realizes that they are Mr. Ashland, and that the creator of nanites was responsible for the future destruction of humanity. There were a couple of things that jumped out at me:
I am a bit confused about the Ziggy/Duffy part. Time Portals are highly illegal (in regards to their species), yet their faction carried tools necessary to create a portal? I figured if having a time portal was punishable by death, it would be highly difficult for their species to obtain the materials needed to create one. Another thing is the relationship between Ziggy, Duffy, and the player. I was wondering how much time will pass between the initial introduction of Ziggy and Duffy to the player, because it seems as though Ziggy and Duffy get attached to the player REALLY quickly. With Duffy being dry and blunt, I find it odd how she/he (it?) would be willing to risk her/his (their?) life for an organism they don't know without clearly assessing the situation beforehand.
My other comment is on the second play-through. I really dig the concept, it's just finding a way to make it seem as though the player isn't simply starting over. I'm sure that isn't your intention, it just happened to be the vibe I got after reading the initial post.
All in all, if the game-play is handled right, this will be a really cool game.