B1: Three 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 an empty room. 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 increasing. Back in the main room, proceed north through the gap in the wall 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 come back down a little to the edge of the pitfall that just opened up. Start running to the left. 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 right.
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 by standing directly beneath the lasers where you can't be seen. 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 you can call Jennifer on your transceiver. She claims that an oxygen tank can be found beyond a door. The door on the south wall can be opened with card 7. Indeed, you will find an oxygen tank inside. Now you will be able to safely traverse through the deep sections of water that were previously harmful too 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. If you already rescued Dr. Pettrovich, you can head back to building 2 to explore the water tunnel on the first floor. Otherwise, you'll have to navigate the north forest to make your way to building 5.