A1: You will arrive through the elevator doors, 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, hug the left wall as you move south. By standing directly against the wall, the camera attached to the wall will be unable to detect you. If you contact Big Boss via the Transceiver, he will warn you to pay attention to the cameras. Take the left path down to B1.
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. Activate card 1 and 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 use card 1 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 (note that unlike the MSX version, you may not put it on before you even enter the room since that causes the door to close shut). 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, you should see the camera monitoring the wall above 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. Walk up to the left wall so that the camera can't see you, and open the door to step inside. You'll find another prisoner. This one will inform you that Gray Fox is alive, but he has been captured. When you step back outside, the camera will immediately see you. Fight or avoid the security team that enters, and 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 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 explosives. 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 and 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 two floor tiles above or below them, they won't notice you. You can use this to your advantage by hugging the tops of the wall 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're higher than them. Punch out both guards and proceed to D4.
D4: When you arrive in this room, be sure to hug the top wall, or duck down below the crates before the left camera pans over far enough to see you. Run to the right and 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. 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, 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.
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 back through the gas-filled room (wear your gas mask), and return to B1 to access another door locked by card 2. On your way, stock up on ammo in the northern cell room if you need to.
B1: Take out both guards carefully, and then approach the door on the right with card 2. Inside, you'll find another prisoner to save. When you exit the room, the right guard will likely notice you immediately. Head 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 cell door and use card 2 to enter. Inside, you will find a new item, the silencer. After collecting it, you can fire your handgun without alerting the guards (the silencer is automatically equipped). While still inside the cell, 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. Run to the east door before the guards have a chance to turn the corner, and open it with card 2 to reach room A3.
A3: Normally this room has three guards, but when you enter from the left, the leftmost guard is removed. Your next goal is to investigate the north door. Open the door with card 2 and step inside. You will find a cardboard box on the floor. This box will conceal you from enemy and camera detection, but only as long as you hold still while you are being observed. Collect it and exit the room. Hug the top wall and knock out the top guard. Then exit east to room A4.
A4: Two guards remain stationary on either side of the elevator doors. Before you hop in the elevator, you'll want to investigate room B4 to the south. You can go down either side of the wall, although your objective in B4 is along the right path. If you choose to use the right path, you'll have to deal with the two guards in A4 to get there. If you choose the left path, you'll have to deal with two guards once you're in B4, so choose either path.
B4: If you came via the right path, you can walk immediately to the door on the right. If you came via the left path, you'll have to deal with the two guards before you reach the door. 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.
You can return north to A4, or you can dispense of the guards in this room and go south to C4 to knock out the electric floor with your remote-controlled missiles. It is unclear whether or not the game rewards you with points toward your next rank by knocking out the electric floor. If you have followed the walkthrough thus far, you have already navigated around this obstacle, therefore disabling the floor is not required to proceed. So, choose to save a missile, or if you want to be thorough you can go to C4 and disarm the floor by firing a missile and guiding it into the brightly colored control panel. Make your way back to A4.
A4: Slip past the guards to reach the elevator. Wait until the right guard is not looking south, then move in to attack him. Then wait for the left guard to look away from your position and run to the elevator. You will notice that you can access more floors from this elevator, including access to the rooftop above (labeled R), and floor 2 below. However, you are not prepared for those floors just yet. Instead, return to the first floor to continue your investigation.