Agent Alpha, a human genius who worked for MiB, went rogue and started grafting Alien DNA and body parts to himself, was one of the biggest series threats in the cartoon. However, there was no mention of him in the films, or two of the novels which continued the first film [I can't speak to the others]. I know the cartoon and movies may not strictly be in line with one another...
So is Agent Alpha canon anywhere else but that series?
Agent Alpha exists in two works; Men in Black: The Series and the Playstation 1 game; MIB: The Series: Crashdown where he appears as a major antagonist (and receives some additional backstory).
Alpha used to be human. The one-time mentor of K, he used to rule the MIB with strength and wisdom, until he went bad. Greed and megalomania caused Alpha to turn against the MIB and ultimately betray K (at one point leaving him for dead). Alpha turned himself into a horrific 'cosmic Frankenstein', traveling the space ways in pursuit of the means to transform himself into the Universe's most supremely powerful being. He has had numerous encounters with the MIB, and although he was captured and imprisoned (in human form), he's been very busy on-board the prison ship, and is set to spring all manner of nasty surprises on Earth...
His existence doesn't conflict with the main film canon. His character appears to be very loosely based on Agent Ecks from the original comics, an MIB character who went rogue and started using alien tech to augment himself.
