A1: You will arrive through the elevator doors, and Big Boss will contact you via the Transceiver. Press F4 to listen to his message, and he will warn you to pay attention to the camera. Two wall mounted cameras slide back and forth on tracks. Your goal is to head south to B1. In order to do it without getting detected by the cameras, and summoning a response team of guards, start by heading south from the elevator doors when the left camera is on its way down. It will go all the way to the bottom of the screen, allowing you to take the right path to B1 without detection, as long as you enter before the camera starts moving back up. However, as soon as you're in the new room, back out and return to A1. The left camera always starts out moving up, so you can safely cross over to the left path way and head back down.
B1: Hug the left side of the wall as you make your way down to the open door on the left. Continue left around the crates as the nearby guard starts moving up along the right side of the crates. Enter the door as quickly as you can. Inside, you'll find a supply of ammo. Just like the rations, this room will always have a supply of ammo in it every time you enter. If you exit the room and re-enter two times, you will have a full supply of 50 bullets in your handgun. Then prepare card 1, and use it on the door below. In the next room, you will find your first prisoner. Simply walk up to him to free him and he will exclaim that he is saved. Some prisoners may have info to relay, but this one does not. Prepare card 1 again and open the door to the right which leads to C1.
C1: As soon as you enter this room, you will begin to lose health. Puffs of gas will rise from the floor and Big Boss will call you on the transceiver again. He will explain that he forgot to mention that you should wear a gas mask in rooms such as these. He will also tell you that Resistance Leader Schneider knowns where you can find the gas mask. His frequency happens to be 120.79 if you want to contact him. Since you should already have the gas mask, you can simply activate it to protect yourself from the effects of the gas (in fact, you can put it on before you even enter the room). Walk around to the door on the south wall, and prepare card 1. Be sure to push down on the door as it opens so you are not exposed to the gas any longer than you have to be. Go through the door to D1.
D1: Upon arriving in the room, a soldier will be walking up on patrol. As long as you stay by the door, he won't notice you, and you can easily sneak up behind him and punch him out. Next, pay attention to the location of the camera by the two doors. The top door is locked with a card that you don't have yet, but the bottom door will open with card 1. When the camera is below the door and it is safe to approach, open the door and step inside. You'll find another prisoner. This one will inform you that Gray Fox is alive, but he has been captured. Step back outside and stay below the camera. Walk below the crates as the guard walks above them, and then head east to room D2.
D2: This room is broken into parts by an interior room in the corner. Enter through the open door. Stand still a moment as the barrels which appear to start rolling right, actually reverse direction and roll back to the left. Wait for them to hit the wall and rebound to the right. When they pass you, run up to the object in the corner of the room and collect it. These are a set of plastic bombs. Wait in the left alcove for the barrels to return and bounce away again. Follow them back to the entrance of the room, and wait for them to pass you again to the left. Then run up and to the door on the right. Once you are back outside, run down the passage while the guard on the other side of the wall is walking up. Then head east to room D3.
D3: Two guards patrol this otherwise empty hallway. Getting past them undetected may look difficult, but it's easier than it appears. Remember that in this game, guards cannot see you unless you are standing directly in front of their line of site. This means even if you are sort of in front of them, but actually a floor tile or two below them, they won't notice you. You can use this to your advantage by hugging the tops of the crates and punching the guards when they get close to you. They are lined up with the middle wall, so technically they can't "see" you as long as you don't go any higher. Punch out both guards and proceed to D4.
D4: When you arrive in this room, be sure to duck down below the crates before the left camera pans over far enough to see you. Keep running to the right in order to intercept the guard that is walking south, and punch him out before he has a chance to walk far to the right. Then approach the lower right door when the lower camera is panning back to the right, and open it with card 1. You'll find access card 2 sitting on the desk. Collect it and exit the room. Immediately move to the left to avoid detection by the camera heading in your direction, and be prepared to punch out the guard again when he gets close enough. If you have used any of your rations and need a resupply, you can use card 2 to open the door below the left camera and find rations inside. Just be careful of the camera when you step back outside. Naturally, your curiosity will lead you to investigate the north path that leads to C4.
C4: When you arrive, you will notice the brightly glowing floor. Big Boss will contact you on the transceiver and advise you to blow up the control panel with a remote-controlled missile. He will tell you that Schneider knows its location, and Schneider will simply say they are in the "southwest", meaning room D1. If you return to this room with a remote controlled missile, you should stand in the safe portion of the floor, and fire one off to the left. While the missile is on the screen, you will control its movements rather than Snake's. Guide the missile through the small maze of crates, and crash it into the small control panel on the left side of the north wall. Doing so will cause the electric current on the floor to stop, making it safe to traverse.
Return south to room D4, and carefully make your way back to the west to room D1.
D1: Back in this room, follow behind the lone patrol guard and punch him out when he doubles back to the right. Wait for the camera to drop below the top door, then approach it and open it up with newly found card 2. Inside, you will find a set of remote-controlled missiles waiting for you on the desk. Collect them and exit the room. Don't stand still or the camera will rise back up and spot you, but don't go to the top of the room or the guard will see you. Stand just above the crates to avoid detection and safely punch out the guard.
At this time, the traditional sequence is to return to C4 and use the missiles to disrupt the electric floor and continue on to B4. However, it is more efficient to pass through the gas-filled room (wear your gas mask), and return to A2 to access another door locked by card 2.
B1: Stock up on ammo if you need to, and then return to the room with the two guards. Take each one out carefully, and then approach the door on the right with card 2. Inside, you'll find another prisoner to save. Exit the room, and head back up to room A1, and then go immediately east to room A2.
A2: Two guards start out at the top of the room, and will each walk down opposite sides of the cell in the middle of the room. Run east to the door and prepare card 2. It's not a bad idea to make sure your health is full before you enter. Inside, you will find four gunmen who are already fully alert to your presence. You'll have to take all four of them out. Each gunmen takes two bullets to put down. Be prepared to hit F3 and use a ration to restore your health if you get hit with too many bullets. Once you defeat all four gunmen, you will be rewarded with a new item, the silencer. Now you can fire your handgun without alerting the guards. Prepare card 1 and approach the door on the right. Enter the next room, and on the table, you will also find the grenade launcher. Collect it, and return through both doors to the room outside. Prepare to deal with the guards by hugging the bottom wall (they can't "see" you there). Punch them both out, and then open the east door to A3 with card 2.
A3: Normally this room has three guards, but when you enter from the left, the left most guard is removed. Your next goal is to investigate the north door. It's a good idea to remove the top guard before you attempt to open the door. Then open the door with card 2 and step inside. You will find a cardboard box on the floor. Collect it and exit the room. This box will conceal you from enemy and camera detection, but only as long as you hold still while you are being observed. Avoid being detected by the guards, and exit east to room A4. From there, immediate head south to room B4 through the right passage.
B4: Walk down to attack the guard that is approaching the door on the right. Then prepare card 1 and open the door. You'll find another prisoner inside. When you rescue him, he will inform you that Diane of the Resistance will support you on frequency 120.33. Diane is very knowledgeable about the various bosses that you encounter throughout the game, so it's a good idea to jot down her frequency so you don't forget it. Exit the room, and return north through the narrow passage to A4.
A4: Once again, slipping past the guards here and reaching the elevator behind them looks a lot more difficult than it actually is. You can run up along either side of the middle wall, and then attack them while hugging the top portion of the wall, where they can't "see" you. Punch both of them out, and step inside the elevator. You will notice that you have a lot more options this time, including access to the rooftop above, floor 2 below, and even a basement level. However, you are not prepared for those floors just yet. Instead, return to the first floor to continue your investigation.