Arduino Due blown. Short-circuit in GND, 3V3 and some Analog Pins

I have an Original Arduino Due and while working on a recent project I successfully wasted it. The 3V3 line is showing short-circuit with GND. I have confirmed that it is from inside the SAM3X8E IC and the voltage regulators are intact. I have already tested that there was no overvoltage applied to any pins (all of the connected pins were outputs) neither any pins were shorted to ground. Also none of the analog pins were utilised.
Then I replaced the Due with a Working Arduino Mega which worked fine. After confirming that there was no problem with the connections I replaced the Mega with a second Arduino Due (original) and it doesn't work anymore. Both the Dues have all digital pins intact the analog pins were affected along with the DAC pins on both. I am unable to find out what the problem was, so please can you suggest me what it maybe ? The dumbest idea may have slipped out of my mind. Please Suggest some possible failure points.

We would need a circuit diagram of whatever the Due is attached to.