I have a 99.5 tdi jetta a night ago I locked my car using my key fob which armed the system I recently went to unlock my car to disarm the system but my key fob did not work so the alarm is still armed I Can open all the doors without the alarm going off it only goes off when I turn the key in the ignition and the car wont start I just need to know how to disarm my anti theft

Door Key Switch
The BCM monitors the door key switches in order to disarm the CTD system. When the lock cylinder turns in order to unlock the door, the switch grounds the disarm input to the BCM.
The key lock input to the BCM is probably missing , BCM doesn't see it . So it think's your breaking into the vehicle. Did you try the passenger door to see if it will disable the alarm .
The BCM - body control module ! Electronic -computer !
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Content Theft Deterrent (CTD) Does Not Disarm with Key Lock

The factory service repair manual has a 23 step diagnostic procedure . An you would need a factory scan tool to find the correct fix.
Turn ON the ignition with the engine OFF.
With a scan tool, observe the door key switch parameter in the Body Control Module (BCM) security data list.
Does the scan tool display INACTIVE?

Locking the Vehicle Without Arming the System
Use one of the following procedures in order to lock the vehicle without arming the system:
• Procedure A -- Lock the vehicle using the manual door lock knobs. Close all the doors.
• Procedure B -- Close all the doors. Use the key or the power door lock switch in order to lock the door. The doors must be closed prior to locking the doors for this procedure.
Disarming the System
In the arm initiated mode, the following conditions are true:
• The security telltale is ON.
• The doors are open.
In order to disarm a system in the arm initiated mode, perform one of the following procedures:
• Press the power door lock switch to the UNLOCK position.
• Press the door unlock button on the key fob.
In order to disarm a system in the arm delay or the armed mode, perform one of the following procedures:
• Use the key in order to unlock one of the doors.
• Press the door unlock button on the key fob.
Deactivating the Alarm
In the alarm mode, the following conditions are true:
• The horns sound intermittently.
• The headlights and the park lamps are flashing.
In order to deactivate a system in the alarm mode, perform one of the following procedures:
• Use the key in order to unlock one of the doors.
• Press the door unlock button on the key fob.
• If the vehicle control module (VCM)/powertrain control module (PCM) receives a valid Passlock™ ignition key rotation.

Disarming an Armed System/Silencing an Alarm
If system arming has been requested by the keyless entry transmitter, it must be disarmed.
Important: Using the power door unlock switch or manually unlocking the doors does not disable the CTD armed mode. Also, disconnecting the battery or pulling fuses does not disable the armed mode, since the BCM stores the CTD mode status in memory.
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To disarm the CTD system in arm pending mode, SECURITY indicator flashing and doors open, perform 1 of the following:

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Press the UNLOCK button on the keyless entry transmitter.

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Insert a valid key into the ignition and start the vehicle.

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To disarm the CTD system in the armed mode:

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Press the UNLOCK button on the keyless entry transmitter.

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Insert a valid key into the ignition and start the vehicle.

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To disarm the CTD system when activated, alarming mode.

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Press the UNLOCK button on the keyless entry transmitter.

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Insert a valid key into the ignition and start the vehicle.

Easiest thing is to chainge the battery in the fob! Sounds like you armed the alarm and now cannot disable! I know in most cars once armed with key it will be on till disarmed! Possibly a batery disconnect for 20 min may run system down and reset! If you can stand the noise!! Good luck

check key fob for stuck button. unhook battery in car to reset alarm. If it has a battery backup on alarm you may need to unhook it to reset the alarm.

stick the key in the door (driver front) and hold to unlock

try unlocking the door with the key driverside first if no results then unlock at the passenger door

The alarm will time out and turn itself off after a minute or two when it is tripped. This turns off the alarm, not just the alarm horn.

Are you saying that you can't unlock a door from the inside by hand?

Normaly you can just Lock the doors and then UNLOCK the DRIVER Door Using the KEY Unless you have Another Problem this will DISARM the ALARM.

The immobilizer feature was tripped when the alarm went off. It sounds like the battery was indeed dead. My Nissan 300ZX used to trip the alarm when I jump-started it, although my Audi A4 does not. When the alarm is going off, you have to disarm it with the key or key fob first, or you won't be able to start it. Try putting the key in the door, lock it, unlock it, lock it again, and unlock it again, just to make sure you get a couple of arm/disarm cycles, then try starting it.

it could be that he locked the car with the key and activated the car alarm try unlocking it with the remote and see if that works