the code is set everytime you turn the engine off, and manually set it - it is NOT/NOT set automatically... in your case, it was set by the gremlin in the dying battery, and my bet is, it was a random, 4 digit number...

As VonBimmer mentioned, there is a well documented time out procedure, in the manual, where you just sit out the timer and then start the car normally - it is done as a anti theft, preventive type of measure...

I use the feature only if i am parked in the area that i am not comfortable with, like gas station where i set the code, then leave the car to pump the gas, and worry that somebody will want to jump the car - i'd just throw keys at him and run for cover... call the cops, while he is trying to figure out what is happening...

the code feature is not good for a quick get-away - so, if you are chased by a T-Rex, it is not a good idea to have the code in the car, as you will lose time entering it, assuming, you still remember, what the fricking thing was!!!