How you wish to use Men in Black in your game fiction is up to you, of course. You should be aware of their variations in American conspiracy mythology, however, if you wish to change or expand their role in your story. Are they agents of some hush-hush branch of the U.S. Government? Clones of the Technocracy? Alien investigators that are actually aliens?
Some reports have them seemingly unfamiliar with everyday objects: fumbling with tableware, trying to drink from the jar of jelly on your table or demonstrating the handwriting of a seven year old.
Some might wheeze and cough as if seriously ill. Others smell bad (inorganic? rotting?), or wear their clothes uncomfortably. Language and syntax may be oddly “manufactured.” Time references are out of date or fractured (“We’ll be back in 1/6th of an hour.” or “Five of the clock, post meridian.”)
Perhaps they use “skin oil jet printers” to plant your fingerprints. Maybe they whisper out of the sides of their mouths at each other, almost simultaneously while interviewing you, as if communicating in code.
Maybe your Men in Black were first seen at the Holloman AFB in New Mexico back in 1964. Are they part of Majestic-12, the department created by Truman in 1947 to exploit the Roswell crash?
Or perhaps something like Men in Black have appeared all throughout history! Are they part of the Technocracy at all? Maybe they are aliens interfering with Earth’s timeline. What a shock to player characters when they trace the same three mysterious figures in black throughout recorded history!
For myself, while I like the version presented in the rule books, I disagree with the decision to make the MiB’s have Arete, i.e. be Awakened. Having an aware Avatar should not be something that can be manufactured, so to speak. So I am inclined to equip my Mysterious Cloned Agents with the latest in high tech equipment (along with enhanced stealth or interrogation abilities?), which makes them scary enough when handled properly, I assure you. When they dissolve into viscous goo after being killed, watch your players’ faces as you describe the process in vivid detail the first time.
For further study, I refer you to these sources: John Keel’s The Mothman Prophecies, Grey Barker’s They Knew Too Much About Flying Saucers, Robert Todd Carroll’s slightly snarky but very useful The Skeptic’s Dictionary, the magazine Fortean Times and, last but not least, both volumes of Kenneth Hite’s marvelous resource for games with conspiracy themes, Suppressed Transmission from Steve Jackson Games.