You posted this in the wrong section... hence it went unseen. Thread moved to the MKIII section.
The factory installed security system is VERY low power. Unless something is significantly wrong with it or it is frequently triggered it is very unlikely to be the cause of the problem. Google how to test for "parasitic loss" with a multimeter and start pulling fuses one at a time until the draw is under a hundred milliamps (around 30 or 40mA is the recommended limit). If it already is then get the battery tested.
Poorly installed aftermarket components are the most common causes of excessive drain: Stereo, amplifier(s), radar detectors, accessories connected to the cigarette lighter (if the cig lighter has been rewired to stay powered when the ignition is off), hard wired radar detectors, etc.
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