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You're now in an underground cave inhabited by wolf dogs who will attack you if they sense you. Meryl will go on ahead of you. Go straight up, and crawl through the small hole in the wall. When you come out, head up to the north-east, into the darker section of the cave. Here, it's a good idea to equip the night-vision goggles for extra visibility. In the dark area, go straight down as far as possible, and crawl through the hole in the bottom-right. Through here, Meryl will be waiting for you at the door. Grab the ration, and enter.
Inside, Meryl will tell you that the area is mined, and mark out a safe path through them. Follow her (or use the thermal goggles to see the mines and find a shorter route). When you reach her, she'll be attacked by Sniper Wolf, FOX-HOUND's best shooter, in an attempt to lure you out. Don't fall for it. Instead, as Campbell tells you, get out of the room and get yourself a sniper rifle. The safest way out is to press against the right wall. To find a sniper rifle, you need to go all the way back to the armoury in the tank hangar. Along the way, look through the area where you first found Meryl in the nuclear warhead storage building floor B1 for items such as Cardboard Box B and some Diazepam, which will steady your aim with the sniper rifle. You'll also find that the canyon where you fought Vulcan Raven in the M1 tank is now several times more dangerous, having been fitted with gun cameras and multiple claymore mines. Using chaff grenades will freeze the cameras, but also your radar, so if you decide to do that, equip the thermal goggles to find the mines. You can crawl over the mines to safely pick them up if you need to. Conversely, the cargo delivery area at the end of the canyon has had its only dangers, the infrared laser wires, removed, so it's now completely safe. In the armoury, you can now access every room, so take this opportunity to stock up on any ammo you might need. The weapon you're looking for, the PSG-1 sniper rifle, is located in the top-left room. The room also contains laser wires and some awkwardly-placed barrels. Equip the thermal goggles and crawl around the wires (you'll need to crawl diagonally to get around the barrels) to get the PSG-1 and ammo (there are 5 bullets hidden behind the barrels on the left). Return to the underground passage to battle Sniper Wolf.
Boss: Sniper Wolf
Luckily, the mines in the front area that Meryl pointed out are now gone. Unfortunately, she is missing too. As soon as you enter, run behind one of the walls, or you'll get shot. If you press up against the wall with your back to Sniper Wolf, you should be able to see a red laser showing Wolf's aim. Wait for her to stop aiming before you try shooting back. Once you're ready, move out and equip the PSG-1, take a diazepam to steady your aim, take aim, and shoot, before she shoots you. She'll either be taking aim at you, or hiding behind a pillar. If she's hiding, watch for her breaths. If you get hit, not only will you lose health, your aim will be knocked off as well. After either you or Wolf gets hit, she'll run and hide behind a different pillar. Once you have Wolf in your sight, don't let her get away. Use rations and diazepam as necessary. After about 7-8 hits, Wolf will go down.
Ocelot's torture sessions
After the battle, save the game immediately, then head up the passage. Look around the platform Wolf was aiming from for some ammo, and head up to the level 6 door at the end of the passage. Just outside, you'll be ambushed by Wolf and a couple of soldiers, and dragged off. After being introduced to Liquid Snake, Revolver Ocelot will subject you to a torture session. What you do during this torture session will affect the ending of the game. To recover your health, press repeatedly, as quickly as possible. To give up, press . If you die, it's game over, and as Ocelot says, "there are no continues", meaning that, if you die, you'll have to start from the last place at which you saved. Ocelot also warns you not to use auto-fire, "or he'll know". This is only half-true; it's impossible for the game to actually know if you're using a controller with a turbo or auto-fire button setting, but if you do use a turbo controller that is quick enough to replenish your health faster than Ocelot's torture reduces it, the game will assume you're using auto-fire and kill you instantly. Depending on the difficulty, you'll have to endure the torture at least three times; each time, the length of the torture increases. If you want to see how the torture session affects the ending, check the spoiler box below:
Escaping the cell
After the torture ends, you'll be thrown in a jail cell. Call Otacon with the Codec, and he'll come to help you as quickly as he can. Depending on whether or not you gave in to Ocelot's torture, you may be called back for further torture sessions. When the guard leaves to go to the toilet, Otacon will come and give you a ration, a bottle of ketchup, a level 6 ID card, and Sniper Wolf's handkerchief. To escape the cell, you have a few options. Wait for the guard to leave the room or fall asleep, and you can either use the ketchup while lying down to play dead, or, failing that, hide underneath the bed. When the guard returns, he'll assume you're either dead or missing, and open the cell to investigate. This allows you to take him out and escape. If neither method works, Gray Fox will come eventually and destroy the lock.
Once you're out, go through the level 6 door and grab the black box with your items. As soon as Snake puts back on his Sneaking Suit, look through the equipment menu with and you'll find a timer bomb. Get rid of it immediately by highighting it and pressing . Use a chaff grenade to disable the camera in the north-east corner, and escape through the door underneath.
You're back on floor B1 of the tank hangar. Just outside are two gun cameras, so shut them off quickly with a chaff grenade, then take the elevator to floor 1 (or B2 first, if you need ammo). Since you now have a level 6 ID card, every room you couldn't access previously is now open, so you can investigate most areas more thoroughly. Of particular interest are the body armour, found on floor B2 of the nuclear warhead storage building, and the cold medicine on floor B1. When you've found those, return to where you were when you got captured. While travelling through the wolves' cave, equip Sniper Wolf's handkerchief to tame the wolves. Head through the level 6 door at the end of the underground passage.
The Communications Towers
Inside, head up and around the corridor. The instant you go through the door, a security camera will spot you. You now have to climb the entire tower while being chased by several soldiers. Killing them is pointless, since more will just come in and begin chasing you instead. Make sure to get the rope here. Run for the next room, and equip the body armour before starting the climb. Realistically, all you can do is run. After every few floors, another soldier will join the chase. If you can, throw him back down the stairs, and he should trip up the chasing pack for a few moments. Also, make sure to use rations as often as is necessary. After a while, you'll find a level 6 door, which is frozen shut, so ignore it. Just keep climbing, and you'll come to a landing; this is the most dangerous part of the chase, since the soldiers now have a clear shot at you. Run around the landing to come to a ladder up to the roof (once you reach the ladder, don't use any rations, since your health will automatically be refilled soon). On the roof, walk over to the bridge, and Liquid Snake will fly in in the Hind D and destroy it. After the cutscene, equip the rope to begin climbing down.
Campbell will call and explain the controls for rappelling. Press to kick away from the wall, and press while away from the wall to move down. Press while holding or to jump in that direction. Hold and move with to walk slowly in that direction. You need to time your movements carefully to dodge the Hind's gunfire and the steam being sprayed at various points. The steam will generally prove more dangerous than the Hind. When you notice steam being sprayed at you, jump away from it. You'll reach the bottom before long. Here, grab the ration to the left, and C4 to the right. You can use the C4 to break the ice holding the door shut, though you don't need to. Next, equip the body armour and Nikita missile launcher. Go as far left as possible, and fire a missile. Guide it across the bridge to the group of Genome Soldiers at the other end of the walkway. Keep attacking them with Nikita missiles until all three are dead. If you try crossing the walkway before they're dead, they'll all open fire at once, decimating your health. Once they're dealt with, cross the walkway. Near the end, Liquid will fly in and begin attacking again. Quickly run into Communications Tower B to the left.
Grab the Stinger and missiles, and go south, through the door. Turn right and go around and down the stairs. At the bottom, you'll find that the stairs are broken. Go back up to the entrance, and this time go down, where you'll meet Otacon, who will go to fix the elevator (this cutscene won't trigger unless you've seen the broken stairs at the bottom). Go right past the elevator and begin climbing tower B. You won't get chased up this one; however, there are some gun cameras after every few floors. Before going up a floor, check in first-person view for cameras, and use a chaff grenade if you see some. The number of cameras increases each time you meet a new group of them, starting at 1 and finishing at 4. When you reach the top floor, run around and grab all of the ammo before going up the ladder.
Boss: Mil Mi-25 "Hind D" attack helicopter
Outside on the roof, Liquid is waiting to attack. Have the Stinger ready to be equipped with before going outside. When the battle begins, put on the body armour and run behind the metal structure to avoid the Hind's gunfire. When the fire stops, check for the Hind's position on your radar (it shows up as a purple dot; move out of hiding if you need to for a clear shot), equip the Stinger, aim for the Hind, and fire with . Stinger missiles are homing missiles, so as long as you've locked on to the Hind before firing (when locked on, the grey target square will turn red, and the Stinger will beep), the missiles should generally hit. Also, the Stinger is aimed in first-person view, so it's a good idea to equip and un-equip it with as necessary. When the Hind's health is down to about 60%, Liquid will launch a missile and destroy what little was left of the bridge to Tower A. Make sure you aren't anywhere near when it hits. He will also start hiding by flying to an altitude lower than the roof, at which you can't hit him. Wait for him to fly back up before resuming your attack. Continue until the Hind's health is depleted. Just before it crashes, Liquid will fire another missile. Avoid it by hiding around the north-west, and watch as the Hind falls out of the sky.
When the battle ends, Otacon will call to inform you that the elevator is working. Head back down, again freezing the gun cameras along the way; this time, you'll have a clear view of the cameras as you go down. Get in the elevator, and you'll hear an ominous warning buzzer. Nonetheless, take the elevator to floor 1. Along the way, Otacon will call and warn you that there were originally five stealth camouflage prototypes, and that the wearers of the four missing ones are in the lift with you. Equip the thermal goggles to find them, and you should then be able to take them out easily with the FA-MAS. When the elevator reaches the bottom, look around on that floor for some ammo and a ration. Go through the door in the south-east, and use a chaff grenade to take out the cameras in this area. Follow the corridor outside to the Snowfield.
Boss: Sniper Wolf
Outside, walk a little forward, and you'll get shot by Sniper Wolf. Otacon will call and beg you not to kill her, but you've no choice. The second fight with her is mostly the same as before, except that she now has more hiding places - namely, the many trees on the opposite side of the snowfield. She'll start out behind some trees to the north-east. As before, once you have Wolf in your sight, don't lose her; though the hill in the centre of the field makes it slightly harder to keep track of her, since she may decide to turn around while running behind it out of your sight. Aside from that, though, she doesn't bring any new tactics, so the fight shouldn't be much harder. Once she's down, walk up to her and watch the cutscene that follows. After, look in the buildings around the snowfield for ammo, rations and Cardboard Box C (the top-right building contains several claymores, and many contain gun cameras). Leave the top-left building for last. Once you've been through the other rooms, go to the top-left one, use a chaff grenade to disable the cameras, and head around the room and down the stairs. Change discs when prompted to begin Disc 2.