Hello -
After a few hours of tinkering with a fairly complex bit of circuitry (that I'm not going to get into here most likely) I noticed my Due behaving weirdly.
When powering over USB, it connects, the LEDs turn on (as normal), but quickly dim and then turn off. My PC makes the "device disconnected" tone.
There is a slight discoloration under the Programming microUSB port.
When I power up using a bench supply, I draw 700-800mA at 9V - this seems really high to me, but the lights stay on continuously. This power is given via the barrel connector, and the ARM chip seems to heat up fairly quickly when powered on.
Any ideas for what may have broke (and ideally, a repair?) I'd rather not have to source a new Due.
You probably fried the processor. However, it's worth checking for other things. Let it cool completely for 5 minutes. Turn it on and start (carefully!) feeling around for hot spots with your fingers. You'd be surprised what you can find out that way.
I assume you disconnected it completely from your mystery circuits.