1) Get out of the air shaft as quickly as possible. Don't shoot anyone in the bathroom. When you get out of your stall turn on your remote mines and exit the bathroom.
2) Once you leave the bathroom, go down the stairs and you will see the door to the console that opens the remotely locked security door. To the right you will see the wall be flat then come out and then go back in. Run up to the hump and place a remote mine on it. Back away and press A and B together to detonate the mine.
3) Turn around and run under the stairs to the door there. Open the door and shoot the guy standing there. Make sure you got the key and then run back out the door you came in.
4) Run over to the door with the console that opens the remotely locked security door. Go in and activate the console.
5) Exit the room and run to the door it opens once you go through that door, go through the door directly infront of you. When you open the door three guards will start shooting at you. Use the walls that come out as protection. and make it down to the other end.
6) Once you're at the end of the hallway open the door and then back into the corner. Once the doors open run through it. Open the door infront of you and back into the corner while you are waiting for the door to open. Once it opens run through it and turn left.
7) Run down that hall and shoot the two guys in it. That should alert a guard on the other side of the door you can't open. He will open it for you. Run through it and turn to your right and run up the stairs.
8) Run down the hallways until you get to the scientists labs. Turn to your right and if your lucky Dr. Doak will be there. Run up to him and then run down the hall behind you. You don't have to stay there and wait he will give you the door decoder anyways.
9) When you're at the end of that hall turn left and throw a remote mine on the wall next to the two guards run past them and detonate the mine.
10) Select door decoder from your inventory and go up to the locked door and press Z. While your waiting for the door to open, make sure no one is behind you getting ready to shoot. Once the door has opened run through it and down the stairs.
11) First contact Trevelyan. Just walk up to him and he will start talking.
12) Don't wait for Trevelyan to finish. As soon as he starts talking Start blowing up the tanks. Start at the end that Trevelyan isn't at and work back to where he is. Throw a mine in between four of the tanks and press A and B at the same time to detonate it. This should destroy the tanks. Do this to the six remaining tanks and then exit through the double doors.
To see a quicktime movie on how this is done, click here.