I just played through the level and beat it in one run. Well, after dying a few times. : D
What you have to do when you run into the first locked door in the Vivarium is to go to the left towards one of those platforms that run across the trees, but this one is on the ground, forming some sort of ramp. Go through there and get into another part of the building. There, doyle ( i think thats his name) will tell you that you need to find a scientist that has a keycard which opens all the doors in the building.
After running into some monkeys on steroids (and some mercenaries on steroid too!), you will find the scientist inside a lab room. The room you go to right after another room where you see a trigen escaping through the celinig. Get the keycard from the dead scientist, and go to another room with a window which has a lever. Pull that lever to open a gate, from which you can escape in a cool a$$ truck. From then on, it's just another quest to get another "keycard", in the form of some explosives to blow up a side of the bunker wall which you need to enter. It's pretty straightforward this area of the level. When you enter the bunker, the level ends. : )