Unplugged antitheft box
 

While doing some interior and pedal work, I had disconnected the anti theft box. I forgot I had it unplugged when I tried to start the car and it of course wouldn't start. I plugged it back in, tried to start it, and the power in the car goes out accompanied by 3-5 soft clicking noises by the fuse box I think.

Now there is still no power in the car (for instance, the power windows don't work, the small light by the key doesn't turn on anymore, etc.) but when the key is in but in the off position, there is a really weak sounding alarm noise.

I tried locking and unlocking the driver door, but it still won't do anything except make that faint alarm noise when I put the key in.

By the way, I do have some other things unplugged at the moment (HVAC system and some other minor stuff), but I'm not sure how that would affect this unless it has some special ground somewhere that I unplugged.

Any ideas? Thank you!

I'm a little confused here... Charge the battery, plug everything back in, arm the alarm and then disarm it? I'm not sure if I'm missing something else or if you're just making it more complicated than it needs to be. There's information on the removal of the security system in the MKIII FAQ section too.

Thanks, but I'm quite sure this is not a battery issue; I suspect a relay or fuse blew or this is something with regards to the theft system. There is no power inside the car and I heard a clicking noise when I tried to start it. Now there is still no power and I hear a faint siren type of noise whenever I put the key in.

So, what would cause this faint noise whenever the key is in (but not turned on) and would explain the lack of power to the inside of the car?

EDIT: I went to try your advice (what did I have to lose?) and the power inside the car was back on, which then led me to believe you were right.. and you were! Thank you! Apparently the last time I drove the car was longer ago than I thought.

The stock alarm system doesn't cut power to anything except for the starter. If you hear the siren but it's quiet the only possibilities are: a poor ground at the alarm or siren, insufficient current (low battery), or a damaged module. As there was little power to everything else the battery was the only significant possibility.

thanks for the info!