The chip inside the key idea is the PATS system... (PATS = Passive Anti Theft System).
It means that aslong as a known chip is near the ignition, the car will start. When you have a key that has no chip (or an unrecognized one), even if it fits, and will turn, the car will refuse to start. So having your 'regular' key with you, and a non-chip key in the ignition will probably start the car. Remove the 'regular' key, and your car will basically refuse starting.
I did have it with my 99 Cougar once. Using an unrecognized key to start the car and finding it didn't wanna start. Well, then we use the 'regular' key (which I put away on the rear-seat to make sure the spare key would start the car). Great surprise when the car wouldn't start with that one aswell... Needed to wait 30 seconds before the system reset itself, and I could use the 'regular' key to start the car. I did take care of that faulty key pretty soon after that tho
Of what I know of those things it's not something that's prone to actually be damaged. So I doubt you really need to worry about that. A Ford dealer would be able to provide you with a proper key for your car and the page below (aswell as your manual I recall) should provide you with information on how to program the thing. Or take the easy was and let the dealer do it for you :P
There's a bit on PATS and the programming of keys on this page: Program a new Ford PATS Key
That doesn't really explain the fact the car died completely when you never messed with anything electronically. Indeed the most likely cause would be a loose wire, or some system reset. If it actually is the PATS system, that page should help you out.
I'm not sure if the computer would throw a code out on the AntiTheft system engaging, but if it does, you might want to try and get a read-out of the computer. It might specify the exact cause of the problem.