James Moriarty, better known as Professor Moriarty, is the main arch-enemy of Sherlock Holmes. In a holo-shed simulation on the Nimbus, he, along with the rest of Zapp Brannigan's History's Greatest Villains, came to life.
This is similar to an event in Star Trek: The Next Generation, where Professor Moriarty (a Holodeck simulation) became self-aware.
He was later ejected from the Nimbus due to an explosive decompression caused by Zapp shooting a laser inside the bridge despite being warned by Attila the Hun. While it is presumed that this event would have killed him, Moriarty may have been brought to life again after in another instance of the simulator malfunctioning. This can be guessed based on the fact that Evil Lincoln who accompanied him in the first malfunction later appears back on the ship in Kif Kroker's room.