There are 5 targets that should be bombed, one in each part of the ship(plane). They are:
the water tanks
the air plant
the docking bay
They must be bombed in that very order. To drop a bomb, stand in the middle of the room and press the bomb button on your control panel. The bombs are timed, so you must bomb all five targets before the first bomb blows up. I would advise taking care of the red dust business first. When you have spread the red dust and planted all bombs, escape by pushing the stick up while standing in the docking bay.