With so many power systems operating all at once, there is the danger that something might overheat and start a fire. The Orbiter has an elaborate cooling system that works to make sure that this does not happen. The coolant used is freon, which is commonly used in refrigerators and air conditioners.

The freon flows through looping tubes around the fuel cells as well as the avionics systems in the forward and aft fuselages. As it passes by the electrical systems, the cold freon absorbs their heat. The freon is then cooled by the radiators on the payload bay doors.

The freon also cools the water system, which in turn cools the air in the crew compartment. This indirect cooling system ensures that no freon accidentally leaks into the air the crew is breathing.