CRORQ is a peacekeeping supercomputer developed by the government as one of the most advanced systems of its time. However, not long after its creation, Dr. Wily reprogrammed CRORQ and used it to control robots around the world. Mega Man sets out to defeat the Robot Masters that led the robots and defeat Dr. Wily and CRORQ.
However, some time later, robots around the world began to turn violent again, and Mega Man is sent out again to investigate. After defeating the Robot Masters who led the robot army, Mega Man confronts CRORQ, piloted by an unknown person, and destroys CRORQ and confronts Dr. Wily.
Unused Sprites of the pilot inside CRORQ in Mega Man 3 (PC).
In Mega Man 3 (PC), there is a silhouette inside CRORQ. This is not Dr. Wily, as he is in the next room. When CRORQ is defeated, it explodes, leaving behind no trace of the apparent pilot. Unused sprites show that an unidentified tall man with short brown hair and glasses was originally supposed to pilot CRORQ, and he may have been in a role similar to Dr. Cossack. 
CRORQ can be pronounced sounding like a frog croak; interestingly enough, the super computer has frog-like legs and resembles a frog.