As soon as you go down the service elevator to sub-level 2, go up to the boxes on the right of the elevator doors, jump up all the way on top and then jump up into the pipe. Crouch and move through the pipe, and as you go the pipe should bend and crimp as you go. Go until you get into the small room, and then go back out the pipe -- the scripts will interpret as you going this way normally, and thus you can easily skip the chase scene/first boss in the refinery.

not a bad...umm...cheat.