Vehicle will start with remote but not with key. the theft light flashes with key

Question edited to add in 'year make model'.
Question moved to model category.

Jeff Armer is the Expert Auto electronics Expert on the site, but I found two ways to reset the Security System and Immobilizer.

https://www.google.com/search?q=2008+ford+fusion+security+reset

1. Insert the key into the driver's side door lock.
2. Turn the key once, but not all the way to unlock the door. Leave the key in this position for 40-60 seconds. ...
3. Do this again, but turn the key in the opposite direction.
4. Remove the key from the door, get into your Ford, and start the engine. The system should be reset.

How to Reset the Anti-Theft System on Your Ford

Focus and Escape resets.

you dont/cant by=pass if using key to lock and unlock vehicle and key is good [starts vehicle ] when you enter you have about 60 seconds to put key into ignition and start vehicle --and make sure have a fully charged battery -- buy a fob online and you can program your self unless it has remote start then need dealer to hook up and flash

Ok disconnect the battery cables like you were instructed in the first answer the when you reconnect them the vehicles alarm will go off when it does use your keyfob to shut of the alarm and it will come out of theft mode and start if you don't do this you will have the same problem no start then when you first put the key in turn it to on but don't crank the motor this gives the self test for the computer to start and you'll see dash lights for check engine and other sensors go out and you will here the fuel pump energize now crank and start give it 10 minutes running to relearn the sensor values then drive the car ok please make sure that there is nothing hanging on the shift lever and you only have 1 chip key in the car with you otherwise it will pick up both chips and will not start good luck stephen

Your vehicle has two theft systems - content theft , if the door is opened without the key or keyless entry key fob the horn honks lights flash . PATS - passive anti-theft system ,this keeps the vehicle from starting if the computers don't see the right code from the transponder pellet in the head of the key .
You can turn off the content theft but not the PATS , when trying to start the vehicle does the theft light flash fast ? Red light on top of the dash .

02 Ford Taurus Anti-Theft problem? - YouTube

? 1:04
www.youtube.com/watch?v=tLYhlnWaZVw
Apr 11, 2014 - Uploaded by Devin Jarrett
Have you tried to force the starter to turn over? ... 2008-2012Ford Escape No Start Theft Light Flashing Diagnostic Walkthrough - Duration: ...

Wrong key , problem with the system , codes stored in the theft module etc... Does the vehicle engine crank but no start ? You need to take to the dealer or a ASE certified repair shop !

Hi Eileen , How do you know your having a anti-theft system problem ? Any lights flashing when you try to crank the vehicle ? The engine does not crank over ? If it is a anti-theft system problem ,disconnecting the battery is not going to do anything except lose some learned setting's in some control modules . There are a few thing's you can check but if none of these are the problem your going to have to have it towed to the dealer ! It'll need to be checked for DTC'S - diagnostic trouble codes !
PATS disables the vehicle from starting if there is:

• a damaged PATS key.
• a non-programmed PATS key.
• a non-PATS key (key has no electronics).
• damaged wiring.
• a damaged transceiver.
• a damaged instrument cluster.

Inspection and Verification

1. Verify the customer concern.

1. Visually inspect the following for obvious signs of mechanical or electrical damage.

Visual Inspection Chart Mechanical Electrical

• Large metallic objects, a second passive anti-theft system (PATS) key on the same key ring as the PATS key, or electronic devices on the key ring that can be used to purchase gasoline or similar items
• Ignition lock cylinder
• PATS key
• Use of a non-PATS key or incorrect PATS key
• More than one PATS key on key ring
• Remote start system installed

• Smart junction box (SJB) fuse(s):
  • 13 (7.5A)
  • 23 (7.5A)
  • 26 (7.5A)
• Circuitry
• PATS transceiver
• Ignition switch
• Instrument cluster

You may not know where some of these things are located !

the issue is the securilock system I installed one in my 03. You need a spare coded key (one that starts the vehicle) and a Bulldog 791 kit. ths will store the spare key and tell the vehicle it is not being stolen. Its the only way unless you want to leave your key in the ignition. BTW, the Theft light is on when you engage the remote started w/o the key in the ignition, Been there.

The chip is in the key. Either the key has lost it's program or the transceiver is not recognising the key. Try another key if you have one.