Well, I battled Mia after finding a way to her in a maze of destruction. Lost air at one point. Also ran out of ammo and had to resort to my pistil. Ahh, good times. Now with Mia killed, I took her fusion cell so that I can reprogram Klein's ship.
Alright! It was tough as I had a hunter alien on my heels the whole time, but I was able to reach Nicole, who was attached to the Marker. I defeated her (eventually) and made my escape with Ellie. What a cool game. Final boss and game ending! Great stream!