REX fires a modified IX Cruise AGM-129 ACM nuclear missile, which houses a W-80-1 variable-yield thermonuclear warhead. These range anywhere from 5 to 150 kilotons. A kiloton is roughly 1.184 x 10^12 (that's 12 zeros) of TNT, and I wanted to allow REX it's maximum potential (it could scale back if it wanted to, naturally). The corebook notes two hand grenades as Energy Blast +6 effects, so I knew a grenade was roughly 6 ranks of punch. A grenade is also roughly .35 of TNT. Throw in a little math, and a thermonuclear warhead should be a bit over 36 trillion times 1 rank of effect in M&M. Using the multiplier table I was able to bring that down to a nice, neat rank 45 power.
...and the stats:
Stealth Nuclear Warheads: Disintegration +45 [Extras: Blending, Dazzle, Explosive Blast (Extra: Super-Area +15 (x32,768)), Neutralize (Extra: Nullification; Flaw: Limited (electronics)), Piercing; Flaw: Device, Heroic Effort; Cost: plot device (195)]
For use in non-Metal-Gear games just remove Blending. I recommend leaving Heroic Effort because when 2nd Edition rolls around it means that while the villain fires the nuclear missile there's good news... you get a hero point.