I see some of my questions and your answers have been resurrected. Unfortunately, my post containing the links to other posts at Apple Discussions which seemed connected has not. I don't know why it was deleted. (I didn't get an email and I can't imagine it violated anything. Maybe an error?) Anyway, unfortunately, I didn't bookmark the links which I'd found after going through a bunch of search results.
If you have earphones, disconnect the speakers and connect the earphones. If the alarm is coming from the speakers, it'll go through the earphones. If not, it is coming from the hardware.
I know I'd said to be careful about backing up because some of the posts I'd found linked alarm sounds with failing HDs. I had hoped you would be able to read them to see if the sounds you're hearing relate to the sounds reported there - which is why I asked if you'd ever described it. I know you said it sounded like your alarm clock. What does your alarm clock sound like? E.g. does it beep, sound siren-like, sound like a smoke alarm...? Some of the posts I found
did mention alarms which sounded even if the computer was shut down and, indeed, even if the computer was shut down, the AC pulled, disconnected from the net, and the battery pulled. Since these were the only links I'd found which mentioned anything like this (after a fair amount of searching), I posted them even though they were not exactly like yours. There was only one mention of a sound repeated at regular intervals and that was repeated at 3 minute intervals even if the machine was shut down, the power and battery pulled etc.
I'm thinking this is one of two things. First, hardware - there are reports of mechanical sounds which sound more like alarms than they do like (obviously) mechanical sounds. These tend to be related to the imminent demise of something - especially hard drives. I say "these tend", but I should emphasise that I only found three links and there was no obvious consensus or pattern. Moreover, it is not clear that the cause was a failing HD in those cases - there are also suggestions linking the issue to sleep settings, PMU etc. There were also suggestions that the 3 minute repeated sound (which I think was described as beeping rather than the "siren-like" alarm in one of the other threads) was linked with a dodgy logic board but, again, it is very unclear - especially since the computer started and performed just fine which is not something you'd expect a computer with a dodgy logic board to do... But I am also forgetting all the details, I think.
Second, something very low level e.g. in Boot ROM or something. (I don't know much about this stuff so I don't know how likely or unlikely - or impossible - it might be.)
I wish we hadn't lost the trail of this discussion. I'm hoping if BDAqua happens by he might know what happened/why it happened so that we can avoid it repeating. I've copied your email in case something happens again because it may get deleted if somebody appropriate happens by to do so. (Since it is personally identifying information.)
The problem with the hardware theory is that unless you have some very strange hardware it is extremely unclear why something bad should happen or be about to happen at 2am, and only 2am, every day. Also, if it comes from the speakers, this isn't it - at least, it isn't a mechanical sound in that case. I suppose it could be an alarm triggered by a hardware issue.
Wish I could remember what I'd searched for, too. I ran so many searches about this that I can't remember the terms I put in the one that finally returned some somewhat relevant results. It still got me 4 pages of results to go through but that was at least manageable. Sorry. I'm not saying the links would have helped, but I'm really frustrated you can't even look to see if anything clicks!
- cfr