Boss Fight: Sniper Wolf
Make your way down the long walkway. Along the path you'll find PSG1 ammo, and a ration near the end of the path on the right, guarded by a gun camera. At the base of the catwalk area, you'll find another ration, PSG1 ammo, and FAMAS ammo at the lower level. Up the stairs, you'll find M9 ammo and SOCOM ammo. Save your game here, because the choice you make next will affect the ending of the game. You may want to come back to this point and replay the game to see the other ending. Approach the doorway to start a cutscene.
Key Items: Ketchup, Lv 6 key card, handkerchief
After much yapping in the cutscenes, you find yourself strapped to a torture device, controlled by Revolver Ocelot. He shocks you, which will drain your health. Simply mash the A button to counteract the torture and bring your health up. You can choose to submit to the torture, by pressing start + A. Or you can choose to withstand it as best you can.
Spoiler Warning: Skip to the next paragraph if you don't want the ending spoiled for you. If you persevere through the torture, Meryl lives at the end, and you earn the bandanna item when you replay the game. If you submit to the torture, Meryl dies, and you end the game with Otacon as your partner through the last chase scene. He gives you the stealth camouflage suit.
After the torture scene, you end up in a prison cell. The guard watching over you seems to have some digestive issues. Give Otacon a call. When the guard runs off to the bathroom, Otacon sneaks in and gives you ketchup, rations, a Lv 6 key card, and a handkerchief. Before the soldier returns, lie down on the ground, and use the ketchup. The guard will open the door to investigate. Stand up and beat him up after the door opens. Run back toward the torture room. There are rations on the other side of the prison cell if you need them. Grab the large box next to the torture machine, which will give you all your items and weapons back. Leave the room via the top right door.
You're back in a familiar spot, but it's guarded by cameras now. Carefully make your way to the elevator, and get back to the tank hangar. Your goal is to backtrack all the way back to the door where you got captured in the first place. Optionally, you can go first to the Armory South area, east of your fight with Revolver Ocelot, to pick up the camera.