I have a clifford matrix rsII installed in my car and it disable my ignition system, i cannot start my car anymore and also my power lock and window are disable as well, I would like to know the best possible solution to enable the system. I dont have the remote and owners manual i do have only the factory remote key button of my car.

When the anti-theft system in your car is activated, it is designed to prevent unauthorized access to the vehicle and protect it from theft. The specific features and functions affected by the activation of the anti-theft system can vary depending on the make and model of your car. However, here are some common ways in which the anti-theft system can impact your vehicle:

1. Ignition Interlock: In many vehicles, the anti-theft system can prevent the engine from starting or cut off power to the ignition system. This is often the primary function of the anti-theft system to deter thieves from driving the vehicle.
2. Key Removal: Some anti-theft systems can also lock the key in the ignition switch, making it difficult or impossible to remove the key when the system is activated.
3. Door Locks: The anti-theft system may lock or unlock the doors automatically when it is activated. This can be intended to prevent unauthorized entry.
4. Windows and Sunroof: In some cases, the anti-theft system can disable the power windows and sunroof to prevent someone from gaining access to the interior through these openings.
5. Alarm Activation: If your vehicle is equipped with a security alarm system as part of the anti-theft system, it may activate the alarm if unauthorized entry is detected or if someone tries to tamper with the vehicle.
6. Vehicle Immobilization: Some advanced anti-theft systems can immobilize the vehicle by cutting off fuel or electrical power to the engine.

If you're experiencing issues with your key not coming out, windows not rolling down, and the sunroof not opening, it's possible that these problems are related to the activation or malfunction of the anti-theft system. However, it's essential to consult your vehicle's owner's manual or contact the manufacturer or a qualified automotive technician for specific information about how your vehicle's anti-theft system operates and to diagnose and resolve the issues you're facing.

In many cases, anti-theft system problems may require specialized equipment and knowledge to diagnose and repair, so seeking professional assistance is often the best course of action.

Passlock™ System
The Passlock™ System is provided in order to prevent vehicle theft if the ignition lock cylinder is forced to rotate or the ignition switch is operated while separated from the ignition lock cylinder case. If starting is attempted without authorization from the Passlock™ System, the powertrain control module (PCM) will disable engine starting. Start disable may be in the form of fuel disable or starter disable, depending on engine application.
The components of the Passlock™ System are as follows:
• The ignition lock cylinder and key
• The ignition lock cylinder case, including the Passlock™ sensor
• The ignition switch
• The body control module (BCM)
• The security indicator on the instrument cluster
• The powertrain control module (PCM)

You can not by pass anything , system will not let vehicle start

http://www.clifford.com/Support/Guides.aspx has the manuals for their products.

Anti-theft system isn't allowing it too .
The Passlock™ System is provided in order to prevent vehicle theft if the ignition lock cylinder is forced to rotate or the ignition switch is operated while separated from the ignition lock cylinder case. If starting is attempted without authorization from the Passlock™ System, the powertrain control module (PCM) will disable engine starting. Start disable may be in the form of fuel disable or starter disable, depending on engine application.
The components of the Passlock™ System are as follows:
• The ignition lock cylinder and key
• The ignition lock cylinder case, including the Passlock™ sensor
• The ignition switch
• The body control module (BCM)
• The security indicator on the instrument cluster
• The powertrain control module (PCM)

Umm, disconnect it's power at the battery? Alternatively, you could put it in valet mode so that all of the convenience features are still usable. The manual tells you how. Clifford XL1000 User Manual

That is because of the vehicle theft deterrent system ! Do you have a security light lit on the instrument cluster ?
The Passlock?"¢ System is provided in order to prevent vehicle theft if the ignition lock cylinder is forced to rotate or the ignition switch is operated while separated from the ignition lock cylinder case. If starting is attempted without authorization from the Passlock?"¢ System, the powertrain control module (PCM) will disable engine starting. Start disable may be in the form of fuel disable or starter disable, depending on engine application.
The components of the Passlock?"¢ System are as follows:
?€¢
The ignition lock cylinder and key

?€¢
The ignition lock cylinder case, including the Passlock?"¢ sensor

?€¢
The ignition switch

?€¢
The body control module (BCM)

?€¢
The security indicator on the instrument cluster

?€¢
The powertrain control module (PCM)

Ignition Lock Cylinder Case, Including the Passlock?"¢ Sensor
The ignition lock cylinder fits inside the ignition lock cylinder case and operates the ignition switch when turned by a key with the proper mechanical cut. When the ignition key is used to turn the ignition lock cylinder to crank, start, a magnet on the lock cylinder passes close to the Passlock?"¢ sensor within the ignition lock cylinder case. The magnet activates the security hall effect sensor in the Passlock?"¢ sensor which completes a circuit from the security sensor signal circuit through a resistor to the security sensor low reference circuit. The resistance value will vary from vehicle to vehicle.
If a magnet from outside of the ignition lock cylinder case is used to attempt to steal the vehicle, the tamper hall effect sensor will be activated. This completes a circuit from the security sensor signal circuit through a tamper resistor to the security sensor low reference circuit bypassing the security resistor. If the ignition switch is forced to rotate without the correct key, or if the ignition lock cylinder is removed by force, the Passlock?"¢ sensor will be damaged and will not operate.

Aftermarket remote start systems are notorious for starting concerns due to the fact THEY ARE BYPASSING YOUR THEFT DETERENT FROM THE FACTORY.Definately in the remote start system.Are you using the factory remotes to open the doors?

Now im not sure since the manual says your model has the same alarm system as the 328i and on the 328i you can remove the module to disable by doing the following. you can unplug the control module. It is located under the glove box. Climb under the dash on the passenger side and remove a few screws on the trim panel under the glove box. Theres a black control module with a green connector. There should be a lock tab on the connector. press the lock tab and pull out the connector. The alarm should now be disabled. But if it has the special transponder key this may not work.
But if the only reason you want to disable it is because of the motion sensor setting of the alarm for no reason there is a solution for this. To disable the motion sensor, hit the lock button to arm, then hit lock button again within four seconds to disable motion sensor. Red light on rearview mirror should flash four times, then pause, then start flashing on regular intervals. this is most likely the reason if your having the issue where the alarm goes off every 20 minutes.
If you want to completely remove it below is a wiring diagram taken from the manual for you alarm system.
this is from the manual its the alarm wiring diagram.
Battery Constant 12v Positive Wire ( ): Red/White or RedBattery Constant 12v Positive Wire Location: Ignition Switch Harness
Starter Positive Wire ( ): Black/Yellow or Black
Starter Positive Wire Location: Ignition Switch Harness
Ignition Positive Wire ( ): Green
Ignition Positive Wire Location: Ignition Switch Harness
Second Ignition Positive Wire ( ): Purple/White or Purple
Second Ignition Positive Wire Location: Ignition Switch Harness
Parking Light Positive Wire ( ): Gray/Purple and Gray/Yellow. Use Both Wires. This vehicle has a dual parking light system that will require 2 extra relays.
Parking Light Positive Wire Location: At Headlight Switch
Power Door Lock Positive Wire ( ): White/Red
Power Door Lock Positive Wire Location: At Factory Alarm Plug. The alarm plug is a black 12 pin plug located just behind the glove box.
Power Door Unlock Positive Wire ( ): Blue/Red
Power Door Unlock Positive Wire Location: At Factory Alarm Plug. The alarm plug is a black 12 pin plug located just behind the glove box.
Door Trigger Negative Wire (-): Brown/Gray
Door Trigger Negative Wire Location: At Factory Alarm Plug. The alarm plug is a black 12 pin plug located just behind the glove box.
Domelight Supervision Wire: Turns On With Unlock
Domelight Supervision Wire Location: N/A
Horn Negative Wire (-): Brown/Red or Brown/Yellow
Horn Negative Wire Location: At Steering Column Harness
Tachometer Wire Negative Wire (-): Black
Tachometer Wire Negative Wire Location: At Instrument Cluster
Brake Light Positive Wire ( ): Blue/Red or Green/Red
Brake Light Positive Wire Location: At Switch Above Brake Pedal
Factory Alarm Disarm Wire (-): Disarms With Factory Remote Only. Factory Alarm Disarm Wire Location: N/A
Factory Anti-Theft System: Transponder Anti-Theft System, Requires Bypass And Extra Ignition Key. The 1997 model year vehicle may require a bypass module and an extra ignition key, if vehicle is equipped with a special key from BMW.
Factory Anti-Theft System Location: Transponder At Ignition Switch Tumbler
if you require further assistance please let me know and i will help assist you from there. Thanks, Midwest-Tek

REMOVAL

1. Disable SIR system. (Refer to "SIR Disable/Enable Procedure (For Frontal and Curtain Inflators)".
2. Disconnect negative battery cable.
3. Remove lock cylinder bezel from steering column shroud by carefully prying with thin blade screwdriver.
4. Remove shroud fasteners and remove steering column upper and lower shroud panels.
5. Insert key into ignition lock cylinder and rotate to RUN position. Then rotate ignition cylinder back to ACC position.
6. Depress locking button on side of ignition module assembly with a thin pick-type tool. Slide lock cylinder assembly from ignition module.

INSTALLATION

IMPORTANT: Actuator blade within ignition module housing must be in ACC position to install lock cylinder assembly. If rotated, replace it to ACC position, using needle nose pliers.

1. Insert key into ignition lock cylinder and install into ignition module.
2. Install steering column upper and lower shrouds and shroud fasteners.
3. Install lock cylinder bezel.
4. Connect negative battery cable.
5. Enable the SIR system. (Refer to "SIR Disable/Enable Procedure (For Frontal and Curtain Inflators)".

are you sure its the alarm? and do you have the red key for the car? hondas have a immobilizer and they quite often lose the code by themselfs hence you need the red key to reprogram it. If you dont have it then it may be quite expensive.

If you have the key to disable the alarm I would try that first, small key on the side of the alarm box turn to off and try it again.

Hope this helps