Has anyone ever had their rear hatch window go down by itself? Got home last night from a trip and parked behind the 4Runner. Didn't notice anything amiss as we were unloading. Came out this afternoon and the rear window was down. First reaction was that someone broke in but no glass, the rear tire carrier was closed and nothing missing. Tried raising it with the key and no joy. Started it up and also couldn't raise it with the interior switch.

Can't remember the last time I lowered it, fearing it wouldn't raise again. Didn't have a chance to dig into it, but can hear the motor trying so it has power to it. The glass is all the way down and maybe off the track or jammed. It had a remote but don't think it controlled the rear window. I quit using it years ago because if I used it to lock up, the horn would go off hours later randomly - i.e. 2 or 3 in the morning.

Any ideas, first I've heard of this

sounds like some of the wires at the top of the hatch where they enter the body either broke or split, Timmy the Toolman has a video on youtube describing how to fix this issue

My last 4Runner had the same problem. I never did find any wiring issues. I superglued my rear window down button on my key fob thus disabling it on the key fob and never had another issue. Might be coincidence but it happened a couple dozen times before modifying the remote. Probably not your issue since you don't use your remote, but thought I would throw that out there.

Yeah, was thinking it could be a stray random signal that effected it, or even some douche bags cruising the street with some sort of transmitter looking for something to react.

I'm gonna inspect the wiring, but a cursory look at the harness didn't reveal anything noticeable. Plan is to get the window back up and probably just disconnect the motor, I never use the window (and apparently for good reason).

My old 97' plow truck was doing that, usually during a rain, so I actually reversed the wires hoping it would stay up, it started doing it again?, so I removed the wires from the rear hatch key slot, and that solved it, that key slot has power at all times, cleaning it didn't help..

Well, never did figure out what caused it but took things apart and applied power to the motor and got the glass raised. Unplugged the motor, and no more random opening.

Yes, the same thing happened to me years ago. Turned out to be the very short piece of wiring harness that is between the backside of the key/lock on the hatch and the harness in there.
I removed that short piece of harness. The only functionality lost was rolling the window down with the key. The switch in the captains quarters still will operate the window. I never bothered replacing it.

I found the original post I made...
Ghost in the rear window

I had this issue a few months ago. Window randomly started rolling down while driving in the rain. Turned out the problem was water getting into the key cylinder and causing the windows to roll down. I unplugged it and it's been fine since. Not a big deal for me as I never use that feature anyways.

Pretty sure my key fob has a hair trigger. I would find it open when I was driving my other vehicle. Finally tossed the fob on a shelf inside and has not happened since.