Alarm was going off for a few hours while I was at work, came back and the car was dead, tried jump starting it and nothing, battery seems fine, all the lights/electrical comes on, but the engine won't crank or move at all. When I try to start all I hear is a loud clicking noise. Any thoughts?

battery is still low, leave the cars jumpered together longer or ideally put battery on a charger. Use the posts under the hood to jump start, not directly to the battery.

Also, doesn't the BMW alarm trigger an electronic engine lock?

When my battery went low it happened exactly as you describe. Everything still came on, except for the clicking noise when you try and crank her.

Even with another car's battery connected, it took a few minutes to give it enough cranking amps to finally turn the engine.

Got a new one, no more problems.

Tried jumping it again, now nothing comes on. I can't even get my doors to open with the key when I turn it.

Tried jumping it again, now nothing comes on. I can't even get my doors to open with the key when I turn it.

try reading the owners manual when you get a chance to. put the key in and turn a full 90 degrees in the cylinder lock. also make sure you jumped it properly + to + - to -. also you may have a faulty ignition switch. it could be a lot of things. check the voltage of your battery.

Also, doesn't the BMW alarm trigger an electronic engine lock?
The e39 has newer technology (EWS II or III in this case). You described the older EWS I where you entered a CODE on the OBC. If the CODE was set and someone tried to start the car...after 3 tries the alarm would go off and the car wouldn't start.

Now, there is an embedded chip in the key and an ISN (individual serial number) that matches other components (EWS control module & ECU).
The car will not start (ignition/starter/fuel) are all shut down if the ISN in the key does NOT matches the ISN assigned to the EWS module & ECU.

So, regardless if the alarm went off or not...the car won't start unless he has the correct key. That's another reason that replacement keys must come from BMW...and cost almost $200 (for a master key).

There should be a section in the owners manual that briefly covers the "driveway protection" system. Below is some info from some BMW tech articles:

http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_122_full.jpg
http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_123_full.jpg
http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_124_full.jpg
http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_125_full.jpg

Alarm was going off for a few hours while I was at work, came back and the car was dead, tried jump starting it and nothing, battery seems fine, all the lights/electrical comes on, but the engine won't crank or move at all. When I try to start all I hear is a loud clicking noise. Any thoughts?

Your alarm was probably going off because your battery is starting to fail and its voltage is low. If your car batteries voltage drops to low...it can no longer keep the rechargable battery in the alarm siren charged...thus it goes off unintentionally.

Have you unlocked your OBC? If so, you can do TEST #9 and see what your battery's voltage is. If you get a reading between 10.5-11.5v (continuous) or lower...the battery is toast. If it reads consistantly between 11.8v-12.8v...then the problem is probably the alternator or some parasitic draw on the battery.

There was a recent thread that listed some great replacement batteries that run between $65-$120...I highly recommend the Duralast 49DL (AutoZone) and it runs approx $69. The Autocraft Titanium 49-1 (Advance Auto) runs about the same price too...both are excellent replacement batteries.

If it is your battery...make sure you get the VENT KIT....your battery must be vented to the exterior since it is enclosed in the trunk.

qsilver7 thanks for the info, this is actually something i was wondering, my alarm sometimes goes off for some reason, i will check my battery, can you explain a little but more in detail the air kit?

Air kit? Are you referring to me writing about the vent kit? If so...because the battery is enclosed...the off gases that naturally occur (the bio-chemical reaction produced by the battery creating power) need to be vented to the exterior of the car. Those gases can explode...which you don't want to happen.

If the battery was under the hood...the air circulation removes these gases away...but if your battery is under the rear seat (like in some earlier BMWs) or in the trunk (like in your e39 and my e38)...BMW provides a vent tube that connects to the battery.

Some after market batteries like the Duralast 49DL vents in a different location than the original BMW battery...so they provide a kit that extends over to your cars vent tube.

So which ever battery you get...make sure that you hook it back up to the vent tube. The BMW battery has a small black elbow (don't throw it away if you still have it)...and the Duralast/AutoCraft/Interstate/DieHard comes with an L-shaped vent kit (see images below)

(Vent kit that came with my Duralast 49DL)
http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_82_full.jpg

(battery in my e34 Touring under rear seat)
http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_83_full.jpg

(vent tube at the rear of the battery compartment in an e38 and the little black elbow you should keep in case you get another BMW battery or a battery that vents on the side like the oe battery)
http://memimage.cardomain.net/member_images/1/web/433000-433999/433594_224.jpg http://memimage.cardomain.net/member_images/1/web/433000-433999/433594_226.jpg

(an Interstate MTP-93 hooked to an E38s vent tube)
http://memimage.cardomain.net/member_images/7/web/739000-739999/739005_150_full.jpg