I had a problem with mine a while back...
What is normally meant to happen is when you put the key in the ignition and turn it, a signal is sent out to check if the keyfob is present. If it doesn't detect the keyfob or it is damaged/battery is flat etc, then the immobiliser will not deactivate.
The problem I was getting was that every time I tried to start the engine, I had to manually deactivate the imobiliser because it wasn't detecting my fob. After taking the fob apart I noticed that one of the contactors connecting to the battery was broken. A quick bit of soldering sorted this problem out and it works fine now.