Where did you apply 12 volt?
At "Vin" or "power supply plug" 12 volt should not be a problem.
If you have applied 12 volt to pins "5V" or "3.3V" you may have killed the mega.
12 volt at Input/Output pins may also have killed it.
It may also depend how long 12 volt were applied. ATmegas are pretty robust and have survived when I was abusing them pretty often, if the "abuse" only was "short enough" (a few seconds) 