MJ12 troopers are on occasions described as "private security". It is likely that MJ12's army is under the cover of a private military company (Possibly derived from Belltower Associates, a company that plays a major role in Deus Ex: Human Revolution).
MJ12 troops wear somewhat generic black combat uniforms with grey metallic-looking body armor, black dress shirts, grey leg armor, black pants, and a red XII (Roman numeral for 12) written on the front of their helmets. They also wear black goggles, though the purpose for them is unknown.
Since Majestic 12 technically rules all of the USA, MJ12 Troopers are an ally of anyone other than terrorist and anti-government organizations; they are even seen commanding the US Military. Since UNATCO is the official face of Majestic 12 military operations, they are only seen working together in Hell's Kitchen when the player meets Stanton Dowd.
MJ12 Troopers are comparable to UNATCO troopers, with the exception that they can use more exotic (and dangerous) weaponry. Like most "troopers" they have 100 HP in all body locations and no damage resistances, despite the body armor, meaning they can be easily knocked out, tranquilized or headshotted.
Their AI often strafes in combat, and when they are near death, they will flee.
- An aquatic variation of an MJ12 trooper is the scuba diver.
- In the Brooklyn Naval Shipyards, a friendly MJ12 trooper can be encountered before entering the ship. He knows who the player is, given that he states "You must be Denton." upon encountering him, and will let them pass without incident, provided they do not attack him or his nearby comrades, even engaging in light conversation with the player. This seems to be a betrayal on the part of this trooper, but his reasoning is not given.
- By continuing to go in and out of the Lucky Money map (holding the "backwards" button) you can access, always in the Lucky Money map, in the stairs zone that lead to VersaLife HQ. The elevator doesn't appear, but a friendly MJ12 trooper is standing and he will react if provoked or if he hears shots, even running to sound the alarm and alerting the police.