Captured: After having been caught by the enemy, you will "wake up" inside a closed cell with no doors. Although all of your equipment and weapons have been taken, you still retain the ability to use the Transceiver. When Snake is being captured, the enemy soldiers will place a transmitter on Snake. So first thing to do is open your inventory and select the transmitter. You only have to use it once to get rid of it. This will prevent the enemy soldiers from tracking you and being alarmed when you enter a room with enemies in it.
Big Boss will call you when you arrive. He will declare your infiltration mission a success, and order you to find Gray Fox. He strenuously suggests that you check the walls. The way you do this is by punching the walls. Most of the time, your punches will have a short thud sound, but against one particular portion of the left wall, there will be a more prolonged hollow sound. Once you find this portion of the wall, punch it until it collapses, and pass through the hole you just created. In the next cell, you will find Gray Fox. Rescue him and he will tell you more about Metal Gear. He will inform you that there is only one way to destroy it, and the only person who knows the method is the creator, Dr. Pettrovich, who is being held captive somewhere in the building. With Gray Fox rescued, your next concern is escaping. Once again, you need to check the walls. After a thorough search, you will find that the south wall has a hollow portion slightly to the left of Gray Fox. Punch it until it opens and step outside into room C1.
C1: Your only two choices are a locked door to the north for which you don't have the correct access card, and a passage to the east. Head east to room C2.
C2: As soon as you arrive, a mini-boss will announce his name, Shoot Gunner, and inform you that no one has ever escaped before. You're about to be the first, but you'll need to find some way to even the fight out. Stay on the bottom of the room and punch the right door open. Inside, you'll find a sack containing all of the items you had in your possession when you were captured, including all of your weapons. You should have at least four remote controlled missiles at your disposal, so activate them and leave the room.
Once Shoot Gunner is taken down, prepared card 2 and approach the left door. Inside, you will find access card 3 and some ammo lying on the floor. Return to the room as many times as you need to fill your ammo for the handgun, sub-machine gun, and grenade launcher. Unfortunately, the north door of C1 is not locked with card 3, so you still can not examine it yet. However, the east door of C2 is accessible with card 3, so open it and head to C3.
C3: Once you enter this room, you will notice a dog (most likely a Doberman Pinscher, but possibly a German Shepard) sleeping by the entrance. You cannot punch dogs (presumably because they are too low to the ground,) you can only shoot them. If you do nothing and ignore the dog, the dog will wake up and attack you, so you are better off shooting it. From here, you will explore a 2 × 3 section of basement. The southern door is locked with a card you don't have yet. An elevator to the floors above can be found at A4, but if you are not very thorough, you are likely to miss many of the secrets that are kept down here. Just as you did in the isolated cells, you can punch the walls to listen for hollowed-out portions. However, unlike the cells, you cannot simply punch you way through them. Once you find them, you must instead plant a plastic bomb in the vicinity of the weakness to blast a hole through the wall and explore what's on the other side. Some weaknesses are found in the maze-like structure in the middle of the basement, while others are found on the outside perimeter. Read the following information at your own discretion or continue to follow the walkthrough by taking the elevator up to the second floor.
Ammo supply: The chances are low that you will be looking for more ammo (you can easily collect some in C2. However, if you don't have enough plastic explosives to blast open every weak wall that you find, you'll be in luck as long as you have just one more. Head to room C4 in the south-east corner and take out the dog that attacks you. Examine the southern wall until you find the hollow section, and plant an explosive on it. Pass through the resulting hole to find supplies of ammo and more plastic bombs. Each one you collect gives you five, and if you have two stars, you can hold a maximum of ten.
Enemy uniform: This is very easy to miss, and won't be referred to much until the time comes to collect it. From the south-west corner of the basement at C3, head north. Examine the west wall until you hear a weakness in the wall, and plant an explosive there. The blast will create a hole, and if you explore the room inside, you will find an enemy uniform. It won't come in handy for some time, but you will be glad you don't have to backtrack to collect it when the time comes to use it.
Body Armor: If you happen to visit the basement after you discover access card 4, some time from now, you can use it to open the door along the south wall of C3. Inside, you will find a very useful item, the body armor. Wearing this armor will reduce the amount of damage you take from bullets in half. You must have this item activated for it to be effective.
Bomb-blast suit: The next item is absolutely essential in order to explore the roof and make further progress. The suit that enables you to pass through the wind barrier on the roof is actually contained behind the door in the center of the basement (visible in B4). However, you must find enough weaknesses in the wall to make your way there. Start by punching the interior walls in C3 (just above the entrance to C2) and blast a hole in the wall with a plastic explosive. Head east to C4, and then north to B4. Keep an eye out for a dog that will attack, and remember to switch back to your handgun so that you don't accidentally drop a plastic explosive instead. Continue north to A4, and examine the wall to your left. You should find a weak point and blast it open. Then step into the new corridor and head back south to B4. This time, you must loop around through C4, C3, B3 (where you will likely be attacked by two dogs chasing you through the maze), and A3. When you turn the corner in A3, examine the wall below you and you should find a weak point. Blast it to find a very small opening, and step inside. Continue around to A4, and down to B4 (watch out for another dog). Activate card 3 and approach the door. Inside, you will find the bomb-blast suit.
Once you collect the suit, you must back track all the way through the maze until you reach the outside perimeter again, taking time to stop and deal with any dog threats that you encounter. Then follow the outside perimeter to the elevator in A4, and take it up to the second floor.
At this time, you should be returning to this building from building 2 in an effort to locate Dr. Pettrovich's kidnapped daughter Elen. Please note that this is an expanded view of the same map presented up above.
You will arrive through the elevator in room F4. Make your way around to room H3.
H3: If you have not taken the opportunity to examine the southern door in this room yet, do so now. You will find that it opens with card 4, and inside is the body armor, which protects you from bullets by reducing the amount of damage they inflict. When you're ready, head west to room H2.
H2: This is where you fought Shoot Gunner. Stock up on ammo in the lower left room if you like, and continue west to room H1.
H1: This is where you escaped after finding and rescuing Gray Fox. The north door was previously inaccessible to you, but you can open it now with card 6. Open the door and continue to G1.
G1: A pair of dogs will be resting here. Take them out if they attack you, then activate card 6 and approach the door to the north. Once inside, you won't see anything, but you will actually hear someone crying for help. While your first instinct may be to punch the walls in search of a weak point, be very careful in this room. As you approach the right wall, you are likely to trigger a pitfall. If you do, run away and let it expand. Then return to the wall, and carefully punch various sections of it until you find the weak point. Then plant a plastic explosive on the wall. Pass through the hole you created and on the other side, you'll find Elen. Rescue her and she will thank you for saving her.
At this time, you must return to Dr. Pettrovich on the second floor of building 2. You may attempt to return through the outdoors, but if you collected the flashlight before you left building 2, there's a time saving, but dangerous short-cut that you can take. Exit the cells and return to G1. From here, visit room F1 to the north if you have the flashlight.
F1: Four more dogs guard this room. Deal with them if you have to, and run up to the door on the north wall. It opens with card 1. Step through and enter E1.
E1: As soon as you enter this room, it will be pitch black. The only way to see anything will be to activate the flashlight. With the flashlight you can see how the crates are arranged in the room. What you can't see, are the pitfalls. The bad news is, the next few screens are loaded with them. The good news is, if you die and continue, you will start from this room. All of the pitfalls in this room are on the bottom. From the door, walk straight up. This is likely to trigger the right pitfall, but you will not be in danger of falling in it. Once you reach the crate, you need to quickly run clockwise around it. As you turn the corner, another pitfall should be forming just south of you. As long as you move quickly around the crate, you won't fall. Continue north to D1.
D1: Line yourself up with the left edge of the right set of crates and walk up. A pitfall may form to your left, and another pitfall is present above and to the right of the top row of crates. When you reach that top row, hug the bottom as you run to the left, and quickly turn the corner to go north as a third pitfall forms to your left. Continue north to C1.
C1: Run up the right side of the middle column of crates. When you get to the top, a pitfall should be forming above you. Now you must run to the right, and up as soon as you clear the pitfall, while another pitfall opens up behind you. Under no circumstances should you attempt to cross via the left passage. Continue north to B1.
B1: Be aware that a pitfall will open up at the southern entrance to the path leading up. You'll have to quickly run up along the right side of the crates and turn the corner so that the pitfall doesn't swallow you. As you run left, another pitfall will open up ahead of you, but this one is easily avoided by hugging the bottom side of the crates until you are free to run north to room A1.
A1: Fortunately, there are no pitfalls in this room. Ironically, Diane will give you a call in this room and advise you to watch out for pitfalls. This would make sense if you attempted to rescue Elen by coming through this tunnel first instead of returning to building 1 through the outdoors. Prepare card 6 and open the door, and you will be back in the basement floor of building 2.