my memory is a little fuzzy too, but i do remember that the fan was very important in order to get to the bace commander.
after the big battle in the tie fighter hanger, i somehow found my way to the top of the large cylindrical shaft, and it had a fan at the bottom of it. i think i got to it by using one of the two lifts in that hanger room. if the fan is on, you can gently float down to the bottom, where some more baddies are guarding that commander.
a note, when you do find the commander, you get him to move by pointing your gun at his back. this took me a little too long to figure out, just making sure you dont loose hair.