If your '98-'00 Expi/Navi has the Ford System 3 (or 4) Security System the following applies:
It has a small red light (Valet Button) below the steering wheel, sort of between your knees. Look directly behind that little red light on it's wire loom that goes up under the dash, there is a very small Micro 'Emergency Override Button' about 3" behind the Valet Button on the loom. You'll need a flashlight.
When you find it, insert the key and turn on the ignition so all the dash lights are on - then push the Override Button, the Security System should now be disabled and the car should start.
You may have to hold down the Override Button while cranking the engine over.
---
You can re-set this entire system too.
To re-initialize Ford System 3 (or 4) Alarm System:
Disconnect the battery.
Wait 2 minutes for the module to lose all traces of voltage.
Turn the ignition key to the RUN position.
Reconnect the battery.
Shut the key OFF and press LOCK on the drivers door switch.
Done.
The system should work correctly. If it doesn't then a part of the system has failed.