Part 1
F1: After having escaped through the back door of building 2 with card 7, Snake will find himself at the foot of a desert teeming with scorpions. The scorpions lunge toward anything they suspect is a meal, and instantly sting anything they touch. Getting stung by a scorpion means a slow painful death unless you possess an antidote to the poison. Building 3 may be 20km to the north, but without a device to help keep him going in the right direction, he will wander aimlessly through the desert. In order to have any hope of reaching building 3, you will need to find the compass and activate it as you traverse the desert. Assuming you have a compass, activate it now, and head north to E1.
E1: Even with the compass, you will need to pass through this scorpion infested desert for at least three screens. Do your best to avoid them, and don't hesitate to use antidote if you get stung by one. You can use a trick you used earlier to make getting by them a little easier; run along the left and right edges of the screen. When a scorpion lunges toward you, simply cross over to the opposite side of the screen. Your progress through the desert will not be lost as long as you are using the compass. Keep moving north until you reach an empty screen at D1
D1: At long last, you will reach the opposite side of the desert. Take a moment to fill your health if necessary before proceeding to the heavily guarded entrance to building 3 at C1.
C1: As soon as you arrive, soldiers will begin pouring out of the series of trucks parked in front of the building. There's little reason to fight with them, as they will appear continuously for as long as you stay on this screen. You'll receive a call from Big Boss, and he will instruct you to hop in the right truck. However, if you follow his instruction, the truck will drive away… and deposit you in the courtyard of building 1. (In fact, hopping in the left truck will do the same.) Clearly, there must be some mistake. If you take the time to investigate the other trucks, you will find that the third trucks from the left and from the right take you to the truck beyond the minefield along the path to building 2. The second truck from the left contains one unguarded box of ammo. The middle truck contains two boxes of ammo guarded by three soldiers. The second truck from the right contains nothing. Seeing as how Big Boss's instructions get you no farther, you may as well approach the door to building 3 and open it with card 7. Enter to reach B1.
B1: Three red soldiers will notice your arrival as soon as you enter, and they will summon backup. Clear them out until they stop appearing. You will get another call on the transceiver from Big Boss. He will instruct you to open the door on the left. It opens with card 1, and if you step inside, you will see nothing but a set of crates. If you move a little further in to investigate, a pitfall will open up! Clearly, this is not the best place for Snake to be, and your suspicion of Big Boss may be beginning to increase. Back in the main room, you must find a way to progress deeper into the building. If you try punching the back walls, you may discover a weak point along the right. Place a plastic explosive there to blast a hole through the wall, and proceed north to A1.
A1: Be aware that as soon as you enter the room, a pitfall will open to the right of the crates in the lower center of the room. It's safest to enter this room far to the right. Run up to the crates above, then run left, and head up as soon as you can to avoid the opening pitfall. The next pitfall to be concerned with opens up just below the elevator, but there is plenty of safe space to run around it without being in danger of falling in. Approach the elevator and hop inside.
As Dr. Pettrovich explained, Metal Gear is 100 floors deep inside building 3. Fortunately, you won't have to watch the elevator drop 100 floors, but it will take a while before you reach the bottom where you can actually exit. The map of the floor (as far as you can explore) is shown below to the left.
A2: When you reach the floor, all you will see are two cameras mounted along the north walls, a door to the east, and an open path to the west. However, the cameras are not cameras at all, but laser defense systems. If you cross their path, they will shoot a rather quick laser beam which is capable of removing nearly half of your health with one hit. It is possible to avoid it, but you must move quickly and constantly; stopping for even a fraction of a second will likely get you hit. PS3 version note: it's possible to avoid being shot by hiding in the cardboard box, but you must not move while directly under the laser.
To make matters worse, it's difficult to figure out what access card opens the east door. As it turns out, none of your cards will work. However, if you have four stars when you arrive here, you will actually get a call from Jennifer on your transceiver. She claims that an oxygen tank can be found behind a wall. The safest place to check is the south wall directly below the elevator, and that turns out to be where you will find a weak point in the wall. Use a plastic explosive to blast a hole open, and step inside. Indeed, you will find an oxygen tank. Now you will be able to safely traverse through the deep sections of water that were previously harmful to you.
If you like, you can explore A1, but you will simply find it to be a dangerous room with another door that you cannot unlock for the time being. Simply return to the elevator, ride it back up to the surface, escape the building, and return south through the scorpion desert to building 2. Open the door with card 7, and visit the water tunnel.
Part 2
Once you obtain card 8 from Coward Duck, you should return to building 3 and ride the elevator to the bottom. The map below is an extended view of the entire floor plan.
F3: You will arrive back in this room. Jennifer will still be calling about the oxygen tank, so you can ignore the call. Now that you have card 8, you can open the east door, but watch out for the laser that fire at you when you pass the camera. Inside, you will find a prisoner who will finally reveal that the leader of Outer Heaven has been your commander, Big Boss, all along. Now you know that you cannot trust any instruction that he gives you. Exit the room, carefully pass beneath the two laser-firing cameras, and head west to F2.
F2: This is an especially dangerous room. When you arrive, you will receive a call from Big Boss on your transceiver. He will tell you that the mission is over, and order you to return. He will even go so far as to instruct you to turn off your MSX system. Whether you follow his orders is up to you. If you choose to continue, you must now pass a dangerous threat. The two wall-mounted cameras roam back and forth. There is no room to slip underneath the beams. Many players simply fill up to full health, get hit once by both beams, and refill their health with a ration. If you don't wish to take any damage, you need to do is trigger them to fire, and run past as soon as the first laser beam ends and another one begins. To do this effectively, you should wait for the camera to return to you, and tap along the direction of the camera (i.e. if the camera is returning to the right, tap right as you run beneath it.) This should allow you to safely trigger a laser beam without actually getting caught in it. When you finally make it to the door at the top, open it with card 8 and proceed to E2.
E2: This room is filled with poison gas. Put on your gas mask and you run through the room. You will see a door to the right, but you may also notice a lot of empty wall on the left. You can pass through the door by using card 8, and if you do, you will enter a blocked off portion of D2 where a pitfall will open and threaten to swallow you. Do not enter through that door. Instead, investigate the empty wall on the left. If you punch it, you will find a weak point. Use a plastic explosive on it to advance to the other side of D2.
D2: If you enter through the hole that you blasted on the left side, you will find a route to the door above. However, it is not free from danger; the left side also contains a pitfall shortly after you advance into the hallway. Trigger it, drop back down to safety, and then carefully navigate around it. Approach the north door and open it with card 1 to reach C2.
C2: This is yet another room filled with gas, so put on your gas mask. You may be thinking that there are pitfalls to worry about, but there is in fact a different danger: land mines. The problem is, you can't activate your gas mask and the mine detector at the same time. What you can do is keep your mask on most of the time, and briefly switch the the mine detector to get an idea of where the mines are. Then you can take a few steps safely until you are unsure, and activate the mine detector again to double check your route. Alternatively, you can leave the mine detector activated, breath in the gas, and fill your health with rations, but don't use too many rations up, or you may find the end of the game difficult. Reach the door and open it with card 1 to proceed to B2.
B2: Unfortunately, you will now be in a room with an electrified floor… and no visible panel to blow up with a missile. If you have four stars, Jennifer will encourage you to simply run across the floor and use rations to heal your wounds. You have little alternative, so do just that. Run across the floor as quickly as possible. You can actually make the entire trip in one run without rations if you start as far to the right as possible. But don't take any chances; if your health drops too low, use a ration. Pass through the door to room A2.
There is a hidden panel in the upper left corner of the screen. It is possible to dissable the electrified floor destroying it with a missile.
A2: This is it. You've finally arrived in the room where Metal Gear is kept! Now is the time to put all the information that Dr. Pettrovich gave you to use.
Plant the 16th and final plastic explosive on the right leg.
As soon as Metal Gear is defeated, the security system will announce an emergency and state that the self destruct sequence has been initiated. A timer countdown will appear on the bottom of the screen indicating how much time you have left to escape. There's one final door to the west, so head through it to A1.
A1: Waiting for you in this room is none other than Big Boss himself. He will explain that he assigned a rookie to this mission in order to report false information, but that you have gone too far. If he must die, he plans to take you with him. As the fight between you begins, Diane will call you and confess that she does not know how to defeat Big Boss. Then she will begin to confess something else about the way she feels about you, but then retract the statement and wish you luck.
Once Big Boss is defeated, hop into the elevator in the back of the room. Instead of finding an elevator, however, you will see three ladders that extend up to the top of the screen. You'll have to choose the correct ladder, as the wrong ones end abruptly before you can reach the top and escape. If you remember the advice that Jennifer's brother told you, you should try the left ladder. If you are having trouble and feel that you will not make it out in time, read the spoiler below for a secret trick that you can perform for more time. If you make it up to the top before the timer runs out, you will have successfully completed the game, and will get to view the ending and the credits. Congratulations.
Would you like more time to fight Big Boss and safely escape from the building? There's one item that you have in your inventory that can help you get more time. It's an item you've had nearly all along, but may not have had a use for until now. Press F3 to examine your items, and highlight the cigarettes. Use them as you would use your rations. They will disappear from your inventory, and 2000 extra units of time will be added to the timer, providing you with plenty of time to beat Big Boss and make it all the way up the ladder.