This seems to be a rite of passage for M3 owners: closing the trunk while working on the car with a disconnected battery. In my extensive searching on the forums for advice on how to remedy this situation, I found no solutions that worked for me, but I did find that many others had made this same mistake as I did.
The obvious answer is to use the terminals under the hood of the car to supply power to your car, by hooking up jumper cables to another car or to an external power supply. For whatever reason, this did not work for me, at all. I tried two cars, and two sets of jumper cables, just to make sure those items were not the issue. No dice.
I also learned that the F80 has no lock cylinder on the trunk. Older models may have a lock, and if so you, could be in business.
Some other poor sap on the forums actually drilled a hole through his trunk lid to gain access. That's just crazy. Don't do that. Ever.
The tech savvy solution to this is to tap into the appropriate wire in your car and apply power with an external battery, thus powering the trunk enough to release it. The only writeup I could find on this was for an older model car, and so the wiring schematics did not apply for me. This sounded feasible and likely would have been my last resort, but I would have called a professional to handle this for me, as I just didn't have the patience left to pore over electrical schematics and figure this out.
In my despair I decided that perhaps I could remove enough of my rear seats to gain access to my trunk. Some older models have a "ski access" in the center of the seats that could be your solution - but for newer M3's this is not available. Since the seat releases are inside the trunk, I thought maybe if I could remove every other point of attachment, that I could pivot the seat(s) up just enough to give me access.
The side bolsters and the seat bottom all just pop straight off, and are easy enough to remove. This leaves just the two seat backs. I found a lone Torx 50 bolt attaching each seat on either side. This could be it! I removed the bolts, yanked on the seats...and found that they were connected in the center by a rod, through a hard point welded to the frame of the car. I could not for the life of me figure out how to remove that rod from between the seats. It seemed all was lost.
I started poking around with my phone on the inside of the trunk, through a gap in the seats, trying to take video and see what I could see. It's a new car for me, so I'm not terribly familiar with any cable routing. Lo and behold, dangling in the rear, center of the trunk lid, was the manual trunk release! The largest gap in the seats you can create is at the driver side bottom corner. I stuck a flashlight in that gap to light the trunk, and prop the seat open. I then rigged up a clothes hanger hook, but even at full extension it was not long enough to reach. So I grabbed one of my golf clubs, masking taped the hanger to the club, and was able to then reach the release. Massive crisis, somehow averted.
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