My data: 1999.5 A4 Q 2.8 30v, 5-spd in the US.
now with 72.5k miles

Friday night I returned home at ~10pm. It was about 60 degrees and
light rain (remnants of Isabel). Neither the AC nor the heat had been
run on my ~30 minute drive home.
About 20 minutes after I got home, I heard something in the garage.
It was a high pitched whine, which I assumed was the auxilliary
electric fan.
I opened the hood, since I had never heard the fan run after the car
was off, even on 95 degree summer days with the AC on full blast.

The engine cooling fan was not spinning.

The "fan-like" sound appeared to be coming from the area under the air
filter.

Question:
Is that perhaps the AC/Heater fan that (for some reason) continued
running?

I started the car briefly, then turned it off. The fan noise stopped.

Checking a few times later, I heard nothing.

Next day, the battery was dead. I can only assume the fan (or
whatever) ran part of the night.

I had my T-belt, WP and thermostat replaced at 69k miles, but I
wouldn't think any of that would affect the AC.

Any advice appreciated.