Nuke Building B1
Key Item: Nikita launcher
Get out of the elevator and head to the left and enter the second door on the right. This is the men's room, and sure enough, a soldier is relieving himself at the far urinal. Subdue him quickly, then grab the ration in the back corner and the book in the bottom toilet stall. If you take too much time in here another soldier from the offices to the south will arrive at the bathroom, so mind your time and your radar. Assuming you worked quickly, walk into the offices to the south of the main hallway, and take out the soldier patrolling there. In the top right corner, you'll find the Nikita launcher, a lot of Nikita ammo and some stun grenades. Raid the lockers on the eastern wall for a ration and M9 ammo. You'll also find SOCOM ammo and FAMAS ammo in the center of the room. When you're finished looking, go to the elevator and head down to level B2.
Nuke Building B2
Key Item: Gas Mask
Gas and an electrified floor guard this area. From the cutscene, you learn the location of the electric generator that powers the floor--it's past the laboratory to the west. You'll need to use your Nikita missiles to take out that generator, but there are several gun cameras along the long, twisty path. The easiest thing to do is to use your Nikita to take out a few of those cameras, so they don't shoot down your missile on the way to the generator.
Simply step into the gas filled room, fire one down the long hallway, and then hang a right into the laboratory. If you're going for the gun cameras, just ram the missile into the wall beneath each camera. One is in the back corner to the left just as you enter the lab area. One is to the right of the first camera, just underneath some high cabinets. A third gun is just underneath the door of the third office on the right, inside the lab. You can't take out the last gun camera with the Nikita. Now just steer all the way back through the lab, into the open door at the end of the room, and hang a right, then a left. A short cutscene plays when you've successfully taken out the generator.
Take another breath of air, then run down the middle hallway to the last office on the right. This office is guarded by a camera, so take it out with a Nikita, or just crawl on the floor so it won't see you. Grab the book and gas mask here. Run back out and take another breath of fresh air, and equip the gas mask, which will greatly reduce the rate of oxygen loss in the gassed areas.
You can explore the offices to the left where you took out all the gun cameras, but there isn't a whole lot of interesting stuff. The second office from the bottom has boxes of grenades, there's Nikita ammo in the second office from the top, and chaff grenades in the generator room. You can use chaff grenades to confuse the remaining camera.
When you're all done looting, go back to the intersection of the two hallways, and go to the right. You'll find another door guarded by a camera. Take out the camera or slip past it, then go into the next room. Open the other door in that room to trigger a gory cutscene. Walk through the bloody hallway and into the next room to start a boss fight.