To be clear about this military bunker SE with the implant:
There are 4 keys total, 3 are color-coded keys you find on level 2. The first key (yellow i think) you find outside to help you get inside. Once inside, the elevator does not work yet - you have to pop a Rad-X, bring some RadAway, and run back through the radiated areas past the machinery and into the middle area with the active computers. With high Science, you get long dialogue in computer, and if you're paying attention, you eventually get to the point where it says you now need to power up the generator. So that is the next step: access the terminal pads on the machines in the very back. If it works right, you should see the lights come on, and then you can use the elevator to access level 2. (I hope you used RadAway by now).
Loot is apparently somewhat random. Tonight my friend got ST implant, a Phazer pistol, no PA, no Gauss rifle.