Follow the stairs down to the Furnace and take the S walkway to the W. Press against the wall, and walk N, crouching when necessary to avoid the crane that moves back and forth. Alternatively, you can destroy the crane, using two Stinger missiles, before proceeding across, though this will trigger the Alert phase.
Head down the stairs, avoiding several guards and then exit through the NE door.
If you look to the southeast in first person, you'll find an opening. It is opposite the cargo elevator. You can go though this, navigate the steam room, and find the exit to the west. Crawling though the exit, you'll enter an area with two cameras. Either chaff grenade them, or sneak upto the package behind the three eletrical boxes. Here you will find body armour.
Use the cargo elevator to the N to head down towards Metal Gear's Underground Maintenance Base. As the elevator moves, three guards will jump down and ambush you.
BOSS: Genome Soldiers II
This is similar to the previous Genome Soldier battle, but the guards do not have stealth camo and there is more room to move around.
After the battle, get off the elevator head E to the next elevator. Watch out for the gun cameras and Claymore Mines. Once you get off the second elevator head through the N door.
BOSS: Vulcan Raven
- Place Claymore Mines in his path
- Use Stinger or Nikita missiles from behind him
- C4 (only if you are experienced enough, if not you'll just waste them)
- Stay out of his sight or you will be turned into Swiss cheese
After the battle, exit through the door to the N.
This room is full of gun cameras. Use Chaff and exit through the N door. Alternatively, you can use the Stinger missile to destroy the cameras, and an Alert phase will not be triggered since there are no guards present.
To climb over Metal Gear REX follow this path: ladder to NE -> ladder to NW -> ladder over REX, then take the ladder down on the other side.
Control room to the S. Watch out for the Guard that patrols here. Otacon will tell you how to use the card keys. At this point Snake loses the key and has to travel down to the bottom floor to find it in the drainage ditch. You can use the Mine Detector to see on your Radar where the key is. Be careful, there will be two dots: one is the PAL Key and one is a "Bomb" similar to what Ocelot put in your inventory after torturing you. If you have not submitted to the torture from Ocelot, then the PAL Key will be eaten by a rat and you will need to kill it to retrieve the PAL Key. You can use your Thermal Goggles to see all the items that are in the water.
You then need to return to the control room to input the card, watching out for the cameras. You then have to do two trips to both the Warehouse and Furnace to change the shape of the card key before returning to the control room to input the card in the other two computer terminals. At this point it is revealed that Liquid tricked Snake into arming the warhead by posing as Master Miller. At this point the room will fill with gas. Equip the Gas Mask and call Otacon to get him to open the door. When you exit the room you will see Liquid escaping to the E so follow him. After some dialogue with Snake, Liquid will jump aboard REX.
BOSS: Metal Gear REX
Constantly use Chaff Grenades to avoid REX's missiles, and fire Stingers (which are your only choice for this battle) at the radome. If you run out of Chaff's, try moving toward REX, preferably between the legs, and the missiles won't hit you; be careful of REX's laser and his feet stomping on you. Also, Stingers can deal some serious damage if correctly shot manually. After doing that for a while the Ninja will show up. The Ninja manages to destroy the radome forcing Liquid to fight with the cockpit open. Shoot the missiles into the cockpit until you wear down Liquid, but don't use Chaff, as they are useless at this point. The Stun Grenades are perfect for the second half of the battle.
BOSS: Liquid Snake
Liquid carries Snake to the top of REX for one final showdown. There is going to be a bombing raid that will destroy Shadow Moses. Liquid has also attached a bomb to Meryl that will go off if Snake does not beat Liquid in time. Whether you survived or submitted to Revolver Ocelot's torture earlier in the game will determine if you find that Meryl is still alive or not. If not, you will make your escape with Otacon.
As you head for the garage an alarm is tripped by your companion, you have to hold off the guards until the jeep is ready. Once on the jeep you can use the machinegun to take out any guards in your way. There are two checkpoints where you get stopped on your way out by guards (try shooting at the oil drums to finish them). Liquid will once again return, driving a jeep of his own. Keep shooting at him to prevent him from firing back.
The jeeps will eventually crash out in the open and Snake and his companion end up stuck under their jeep. Liquid then walks up to them to finish them off but dies from the FOXDIE virus at the last moment. Campbell then informs them that the bombing raid was called off and a snowmobile is parked nearby for them to make their way back home.
CONGRATULATIONS! You have now completed Metal Gear Solid.
After the end credits, you will be awarded with a codename based on your game performance and a special item for your next playthrough, either the Infinite Ammo Bandana or the Stealth Camo.