A watchdog is used to detect when a system has gone off with the fairies; you have to reset the watchdog timer ("pat the watchdog") every so often or it takes some recovery action. In the case of the Arduino Due, with the ATSAM3X8E MCU, the recovery action is to reset the CPU.
In the ATSAM3X8E (and probably other Atmel MCUs, too), the
watchdog timeout defaults to 16 seconds, and the default hardware
state is that the watchdog is enabled! (the default in
the Atmel Software Framework is
to disable the watchdog unless you have