Nuke Building B2
Key Item: Body Armor
When you get to the nuke building, stop off on floor B2 to get the body armor. Go back to the lab area where all the gun cameras are/were and enter the office at the bottom, which has a level 6 door that you can open now. Grab the body armor inside, then go back to the elevator, and head to level B1.
Nuke Building B1
Key Items: Medicine, PSG1-T
We've done this drill before. Head to the men's bathroom as you did the first time here, and take out the soldier there. Go to the offices in the south and take out the soldier patrolling in there. This time, you can raid all the locked office rooms for useful items. The office at the top left has another cardboard box and rations. The middle office on the left has the medicine, which is key because you caught a cold while you were locked up with no shirt on. Use the medicine to stop your sneezing, which could give you away as you're sneaking around. Bottom left office has pentazem, the PSG1-T tranquilizer rifle, and PSG1-T ammo. The rest of the area has ammo for just about every other weapon in your arsenal, so top off your ammo if you need to before you continue to the area where you were captured. As you make your way back there, equip the handkerchief in the caves, so the wolves won't attack you.
Communication Tower A
Key Item: Rope
Welcome to disc two. Go down the hallway, grabbing SOCOM ammo and FAMAS ammo along the way. Entering the next door will trigger an alarm. Finally some real action! Grab the stun grenades and especially the rope here. Begin running up the never ending stairs, shooting soldiers with your FAMAS as you go along. Alternatively, you can throw lots of stun grenades if you're trying to kill as few people as possible. Eventually you'll find a door, but Otacon tells you it's frozen shut. Keep moving up the tower, shooting soldiers as needed. The idea is to keep moving, because a never-ending stream of soldiers will whittle down your health if you stop too long to fight. Eventually you'll reach the top level, where you can grab rations, and FAMAS ammo before you come across a ladder that you can use to take you to the roof.
Communication Tower Roof
Walk out to start another cutscene. Liquid Snake will jump you with a Hind gunship. When you regain control of Solid Snake, equip the rope, and you'll begin a brief rappelling sequence. Follow the directions from Colonel Campbell, and make your way down the side of the building. Liquid will strafe you a couple of times, but just descend quickly and you won't take much damage, if any.
Communication Tower Corridor
Key Item: Stinger
You can grab the C4 nearby to blow open the door that was frozen shut, but there's really no point in doing so. You don't want to go back in that direction. Instead, use a scoped weapon, and take a look across the bridge. You'll see three soldiers there. Use your sniper rifle, or Nikita to eliminate those soldiers, then walk across. Liquid ambushes you at the other side. Quickly move to the left and run inside to escape. Grab the Stinger launcher and ammo, then go in the door to the south to enter Communication Tower B.