Firing weapons and running your engines generates heat which must be dissipated through your ship's interlinked cooling system. As your systems heat up toward their maximum of 100their excess heat off into the opposite cooling system. This can be extremely useful when you are desperately trying to escape an enemy trap, and need just that extra boost to get you into home space. Each weapon shot 'costs' given amount of heat which is based on the power of the weapon. Warp drive on the other hand costs an amount that increases as you increase your warp factor. With all of the above interactions taken into account, it is usually possible for a normal ship to pull about warp four and fire weapons before starting to accumulate heat.
In addition to these standard sources of heating, if you are playing a configuration with the teleport option, teleporting costs a large amount.
The cooling systems can only operate at peak efficiency with ship's shields down since the entire purpose of the shield system is to repel energy. With shields up the cooling system will still operate, but at a lower dissipation rate. Similarly, when the ship is cloaked the cooling systems operate at a scaled back rate.
If the ships cooling system exceed 100% capacity, there is a growing probability during each time slice that the system being cooled will shut off to protect itself from a meltdown. The capacity of the cooling system must approach 0% for the system to be reactivated. When a system overheats, a flag is triggered on the status line, W for weapons, E for engines.