http://www.fordwiki.co.uk/index.php?title=PATS_Immobiliser_Fault_Codes
https://www.youtube.com/watch?v=0kBZeBbb9PM
http://passionford.com/forum/technical-help-q-and-a/164706-mk2-mondeo-immobiliser-problems.html
http://www.fordownersclub.com/forums/topic/41159-not-starting-possible-immobiliser-problem/
When the LED flashes you may see a pattern. Watch it next time and you may be able to work out what code it's flashing The code is usually repeated about 10 times and will signify a two number code i.e.- Flash flash pause flash would be code 2,1. These codes assist in diagnosing immobiliser faults. If the light flashes rapidly with a long amount of flashes it usually means the key is not recognised at all.
From Fordwiki-
PATS Immobiliser Fault Codes
Introduction
If a fault develops on a vehicle fitted with Ford PATS there are a series of simple checks which can be carried out before proceeding, if necessary, to the FDS2000 diagnostic programme. There are also a number of self-diagnostic two-digit codes which may be displayed by the indicator LED which indicate a specific fault and could avoid the need to proceed with the FDS2000 diagnostic programme.
Note: The indicator LED must be carefully observed and the sequence of flashes noted.
When the two-digit codes are flashed, for example 1:3, a single flash followed by a break, followed by three flashes and a break, will be repeated ten times before the LED finally goes out.
Fault Finding Procedure-
Fault - Engine does not start or crank: LED does not illuminate
PATS system fuses in foot well fuse box. Fit or renew as necessary.
If alarm is fitted check whether LED functions for alarm: If OK go to FDS2000. If not OK check cigar lighter fuse (this also supplies power to LED).
Fault - Engine does not start or crank: LED flashes rapidly. (Engine is immobilised but key will not cancel immobilisation)
Check: Leave ignition switched on for at least one minute or until LED starts to flash two-digit code. Note the code being flashed and compare with the following list:-
Code Problem Check
1 : 3 Key code not received is the key obscured, try again with different key, key may be damaged/faulty 1 : 4 Partial code only received is the key obscured, try again with different key, key may be damaged or faulty 1: 5 Key not programmed to PATS Programme key 1 : 6 Faulty link between PATS and EEC v module check with FDS2000
Programme key.
Fault: Engine does not start or crank: LED illuminates for 4 seconds and goes out: (PATS is working correctly, possible fault elsewhere in system)
Check: Starter solenoid relay, renew if necessary. If still no start, Go to FDS2000.
Fault: Engine cranks but does not start. LED illuminates for 4 seconds and goes out (PATS is working correctly, fault elsewhere in system)
Check: Power to PCM or fuel pump (diesel), if still no start, Go to FDS2000 Check PCM fault, Go to FDS2000 (Petrol and Gas engines)
Fault: Engine starts but LED stays on
Check: Leave ignition on (engine running) for at least one minute or until LED starts to flash two-digit code 2 : 1 Less than three keys programmed into module: vehicle can be driven but one or two more keys should be programmed into memory.