- Mites - One of the first mutagen based experiments involved Dr. Cray placing a single drop of mutagen onto common insects such as mites and ticks. (EAGLE DEATH and EPICGAMING king1 call them "Puppies")
- Mutants - Are the result of Dr. Cray's research as head of Area 51's Biowepons Division there are several types of Mutants but all Mutants are strong and very resiliant to gun fire.
- Mutant Scientist - Many of the research scientists trapped in the lower levels of Area 51 were exposed to an unknown mutagen. Possibly viral in nature, this mutagen triggered a rapid growth phase, greatly strengthening the skeletal and muscular systems. Similarly, the virus has caused a severe psychosis in all those infected.
- Mutant Security Force - The security component of Area 51 was unprepared for a viral outbreak. Many of them were caught off guard and didn't have time to put on a gasmask. Those infected by the release of the virus mutated rapidly. They seem to retain enough of their humanity to use firearms (SMP or shotgun) in a rudimentary manner.
- Mutant Leaper - As the virus continues to mutate its human host, the victim begins to completely devolve into an animalistic state. The Leaper is the final phase of human mutation and has lost all humanity. Leapers use all four limbs to move and climb surfaces.The Leaper shares somewhat of a mutation process similar to that of the lickers from the Resident Evil franchise,which is also the Final phase of mutation by virus. They possess wicked talons that can penetrate through body armor.
- Mr. White - Mr. White is the Illuminati's representative to the Greys. Originally a scientific peer to Dr. Cray, Mr. White was seduced by the Illuminati and has become Dr. Cray's nemesis. After perfecting human cloning, Mr. White's research was used to create the Black Ops. Mr. White, ever the narcissist, created several clones of himself to ensure a powerbase of loyal servants. Mr. White's cooperation with Grays is carefully calculated to provide him technology and weapons to eventually control the world.
- Mr. White Clone - Mr. White created a series of clones to work throughout the Area 51 base. They use teleportation devices on their wrists to travel around the Area 51 base. They are seen running experiments and interfering with Ethan's progres in Area 51.
- Black Ops - Black Ops are clones humans, the result of Alien/Human DNA recombination. These hybrids have excellent combat reflexes and are conditioned to obey orders from the Illuminati and Grays. The Black Ops carry SMP and occasionally shotguns.
- Black Ops Leader (RED) - Selected Black Ops are given cloaking armor enhancements and spacialized tactical training. Used to command squads of ordinary Black Ops, the Black Ops Leaders are a serious threat and should be eliminated as quickly as possible. They quite frequently are seen carrying a BBG over the SMP.
- Not much is know about the egnimatic Grays. Their first contact with humankind was the result of a scout ship that experienced a malfunction and crashed near Roswell, New Mexico in 1947. They communicate using gestures and telapathy, Rarely encountered, they prefer to dwell in the deep bowels of Area 51 experimenting with captive humans. The exact purpose of these experiments are known only to the Grays and Illuminati counterparts. The Grays don't attack directly, though they are sometimes found behind a shield from where they send out teleportation orbs, which spawn Black Ops prepared to attack.
- Theta - The Theta is the ultimate biological weapon engineered by the Grays to spread a mutagenic virus as quickly as possible to any carbon-based enemy. Theta can communicate with and command Leapers. Equipped with an electro-chemical pulse weapon, The Theta is an impressive killing machine. Rumors within the Illuminati elite talk of a "Super Theta" project.Rumors also go that the Theta was the cause of the Dreamland incident,as seen in a intro cut-scene where a team was ambushed by a creature that resembled the presence of a theta.
- Super Theta - The Super Theta is an improved version of The Theta, it is armed with a modified version of the BBG. The Super Theta is more resiliant to gunfire than The Theta, though alien weapons appear to be more affective.