A1: You've now arrived on the second floor. As soon as you leave the elevator, one of the two top guards may notice you and alert the other three guards in the room. Remove them as quickly as possible and continue on. You have some choices, but the left path leads to a dead-end. Of the two paths to the right, take the higher one to A2 so that you can collect an item in A3.
A2: It's a good idea to remain as undetected as possible in this room, although that can be quite difficult. Try to get a feel for each guards patrol route before you step too far into the room. If anyone is likely to notice you, it will be the guard who patrols the upper right corner of the room. That also happens to be your destination. Clear a path so you can use the upper right hallway to access A3.
A3: Open the door that you arrive in front of with card 6. Approach the desk and collect the antidote sitting on the desk, which you may have need of later. Exit the room and return to A2, hugging the top wall to help you avoid detection. Your goal is to reach B2 in the center of the floor. This can be accomplished by using card 1 to open the south west door of A2.
B2: Assuming you arrived through the north west door, be prepared to move down immediately after you arrive. This room is guarded by two hulking men who are referred to as the "Arnolds" or the Arnold Brothers, and who will rush at anyone who attempts to access any of the doors in the north and south portions of the room. They will not leave their post, however, so you are perfectly safe to stand in the middle. You have no weapons that are capable of defeating these cyborgs, so ignore them for the time being. Instead, prepare card 5, and open the east door to reach B3.
B3: Do your best not to be spotted by any of the guards, and approach the upper left door after knocking out the north guard. Use card 5 to open the door, and inside you'll find a prisoner who has knowledge of a new resistance member, Jennifer, who can be reached on frequency 120.48, but only if you happen to be at the highest (four stars) class. If you've been following along with the walkthrough, this will be the very rescue that will get you promoted to the highest class of four stars. Exit the room, and carefully take out the guards again. The last guard standing still in front of the right door can be easily snuck up on by approaching him from the left. If you enter the room using card 6, you will not find anything inside. Read the spoiler below to learn the secret of this room.
If you take the recently rescued prisoner's advice and call Jennifer from outside the room, she will answer (as long as you have four stars) and inform you that she is preparing a rocket launcher for you. When you enter through the right door, it will be waiting for you on the table. You now have a powerful weapon, but you have no ammunition for it, so you'll need to find some.
Return to the Arnolds' room to the west.
B2: You are still unable to do anything about the Arnolds. With six passages to choose from, the best course of action at this time is to open the lower left door with Card 1, and proceed to C2. Rush to the door and pass through it before the lower Arnold has a chance to reach you.
C2: Remove the guard standing in your way along the left side of the room, and follow the passage around to C1.
C1: Make your way around the walls, taking out each of the stationary guards, and the patrolling guard when it is safe to do so, until you reach the open door in the upper left corner. Once you step inside, collect the three boxes of ammo in the room. Exit and enter the room as many times as necessary to max out your ammunition, and then exit the room. Take out the guards again on your way out, but this time, head north to room B1.
B1: It's difficult to make it across the central passage of this room without getting noticed by one of the three guards, but it's easiest if you hug the right wall as you enter. Whether you are spotted or not, proceed north to room A1.
A1: In this center passage, you are safe from detection from the four guards posted along the outside. Prepare card 6, open the door and step inside. When you step inside, it will appear that at long last, you have found Dr. Pettrovich. However, when you run up to rescue him, a voice will tell you that you've fallen for a trap, and that the real Dr. Pettrovich is being held in building 5. When the speech ends, a pitfall will open up beneath the fake doctor. Be sure to move Snake down when the speech ends so that you race away from the pitfall as it opens up. When it's safe, return to the south, and make your way back to the Arnolds' room at B2.
B2: If you happened to obtain a rocket launcher and some ammunition, you can finally take on the Arnolds.
Once both Arnolds have been struck with four rockets, they will leave their prized possession behind: access card 7. Be sure to collect it before you exit the room. Now you are free to explore any passage you want. Start by using card 2 on the upper right door to return to A2. Watch out for the guard, and follow the path up and around to A3.
A3: Three guards patrol the main portion of the room. Do your best to remove them undetected, and approach the door in the upper left corner. It opens with card 1, but if you enter the room, it will be empty. Once again, this room contains a secret. Read the spoiler below to find out what it is.
Once again, you'll need to call upon the help of Jennifer, the resistance member who won't speak to anyone with less than four stars. If you contact her from the room, she will put an item in the room. Then you can enter and inside, you will find a compass waiting for you on the desk. Collect this important item and exit the room.
When you're done, exit the room and retrace your steps back to B2.
B2: There's only one unexplored passage left. Use card 5 to open the lower right door to C2.
C2: Do your best to get past each of the three guards on the right side of the room undetected, and explore the room behind the open door. You'll find a prisoner who will inform you that you need a compass to cross the desert. Exit the room, deal with the guards again, and take the east passage to C3.
C3: The lone guard that patrols the room has a tendency to fall asleep. Wait until he passes out, and take him down. Then open the door with card 5. Step inside the room, but stop for a moment to investigate the situation. You will see a set of rolling barrels and elevator doors at the far end of the room. In order to reach the elevator, you'll have to time your approach very carefully. As soon as the barrels roll past you to the left, you'll need to race out to the door. Get there as quickly as possible and push up against the door when you reach it. It should open and allow you to enter the elevator.
Hop in the elevator, and take it down to the first floor. At this point, you have two choices. You can choose to visit either building 3 or building 5. You will have to do both before you return to this building. For the time being, use newly acquired card 7 to exit the building and explore the outdoor paths to either building.