Battery Won't Charge, Anti-theft?

[Mhaddy]

Up in the great white north, it's finally time to take our cars out from hibernation and introduce them to the road again. I, unfortunately, didn't remember to put the trickle charger on my battery and so the battery has since drained completely. This morning when I finally put the charger on, I'm hearing a clicking noise from under the hood, seemingly coming from a number of different components and when I open the door, the interior lighting is flashing in a sequence, I think like...

blink-blink-blink-blink-blink-[blinkblink] & repeat

I've since disconnected the charger because I don't want to risk damaging any of the components. The charger manual indicates there may be some 'undue' strain on the battery and suggests removing it... any other suggestions? Any idea what this is/has anyone experienced it before? Thanks!