I recently set off my alarm system while doing some detailing. I unlocked the rear liftgate with a key (I'm not used to having a remote entry thingy yet) and the horn blared. I silenced it by pressing a button on the key fob remote. Not knowing any better, and since it really isn't explained in the Owner's Manual, I thought this deactivated the alarm. Apparently, it only silences it. I guess when I went too long without starting the engine with the key, the computer got the message that the car had been broken into, so it disabled the engine. It would crank and crank, but would not fire even once. After a week of trying to figure out what was wrong, a friend with a professional analyzer (SnapOn) came over and read the codes. He said "This says 'Engine Disabled by Security System,' what's that all about?" I said (nicely, of course), "Please just shut up and clear the code, Pleeeze." He did, and it started on the first spin. Doh!
The owner's manual really doesn't say much about what to do if you set off the alarm. I couldn't find anything about it disabling the engine anywhere in my book.
But I guess I know now!