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Welcome to Ghoul City. The best time for coming here (and the best ending) is sometime before the water chip deadline (well, no kidding) and during the mid game... actually, before 110 days to be precise. There is a mutant threat (unbeknownst to you) to this city if you do not save it in time.
Your main goal here is obviously the water chip, found after some exploration, but other decent items, xp and enlightenment about the Fallout world can be found as well. The main mode of transportation between maps is in the several manholes and ladders spread throughout Necropolis. When in doubt, look for the nearest manhole down or ladder back up to another section. Some of the manholes inside of buildings are covered by walls, so looking for them--especially in the dark--can take a minute or two.
In general, the ghouls here remain non-violent on the inside of buildings until you irritate them but are hostile out in the streets. You can attack them all (save a couple quest ghouls explained below) with impunity. Of course, if you loot their rotten dressers and desks, some of them might attack, but killing them too is okay. In the second surface section labeled the "Hall," you'll find a large church with glowing ghouls held in individual cells. They cannot be freed. At the back of the church is Set, a ghoul faction leader. Talk to him for one of the few quests in Necropolis, destroying the Super Mutants.
Another ghoul you'll probably want to remain friendly with is the underground leader found in the sewers. He'll ask that you repair the waterpump before you go after the water chip, so that they can remain in Necropolis.
- Hotel: the place you enter. Killing ghouls here is okay, and look for several manholes down to the first sewer level
- Sewers: four separate sewer areas in Necropolis. The second sewer area you get to has the friendly ghoul with the waterpump quest. The sewers entered via the manhole next to the captured prisoner at the Watershed is the 1st level of the old Vault
- Hall: the second outside area you get to. Includes the church with a quest from the ghoul Set
- Watershed: the third outside area. The water pump, captured prisoner and Super Mutants are all here in the northeast section
- Living Quarters: the 2nd level of the vault
- Command Center: the 3rd level of the vault. This is where the water chip is
Here is a list of the significant quests in Necropolis, each with a brief synopsis containing at least one way to solve it. The remaining ways, and possibly other minor quests I will leave up to you.
Destroy the Super Mutants:
On the Hall map, reached from the second sewer area via a ladder back up, find the church at the back and talk to Set. If you do not make him mad, he'll give you a quest to kill the Super Mutants in the Watershed area. Accept, go back down to the second sewer area, then exit that area by green exit grid to the third sewer area and take the ladder up to the Watershed. The super mutants occupy the northeast section of the map. I'd suggest having a fairly powerful small gun like the Sniper Rifle, or preferably a shotgun on burst mode for taking them out. The one inside the north building named Lou will talk to you, but do not allow him to take you to the Military Base. That is a dead end that will likely get you killed when you're teleported deep into the base with very powerful mutants likely angry at you. Instead, kill him and his goons in the next room, the super mutant by the pole to the south, the one in the small room nearby, loot 'em and return to Set, where upon your return you'll get a king's ransom in rewards, but I won't spoil the surprise.
After settling up with Set, feel free to kill these ghouls if you wish. An easy way is to run around the church and shoot them through the windows, where they won't react to you, and then pick off the few remaining inside where you couldn't shoot. Then loot.
Fix the Water Pump:
On the second sewer map, reached via green exit grid from the first sewer map, you'll encounter the leader of the underground ghouls. Talk to him, and you'll find out about the water chip, and about their plight to stay alive if the water chip is taken. Agree to find the parts and set off for the Watershed map. Enter the manhole directly south of where Harry the super mutant is/was by the pole. Follow this to the back and you'll find the parts required to fix the pump. Place them into your inventory, save your game, make sure your repair is as high as you can get it, pay a visit to the water pump in the northeast section of the building where Lou was, and "use" your parts on the water pump. With a repair of 50% you may have to retry a few times. When it is successfully repaired, you get 1000xp, but no further reward from the underground leader.
Free the Ghoul Prisoner:
In the northeast section of the Watershed map, in the building where the super mutants were/are, there is a captured ghoul prisoner a cell just south of the water pump. Free him for 500xp, and he'll tell you the location of the vault, which conveniently, is reached by the cell nextdoor to the prisoner.
Find the Vault 13 Water Chip:
In the northeast section of the Watershed map, in the building where the super mutants were/are, there is a room just to the south of the water pump with a hole leading to another section of the sewers. It really leads to the 1st level of the Vault, named Vault 12 (though the game does not tell you this). Enter the 1st level, defeat a couple glowing ghouls who radiate you when they hit (for low radiation that you shouldn't worry about), search the area, and enter the elevator to the 2nd level. Search that area for some more ghouls and 2 Rad-X from a locker, which can come in useful for your next destination (after returning the chip), The Glow.
On level three, hunt for the only working computer, and use it to remove the water chip and receive roughly 1000xp. Use your Science skill on the computer first if you're having difficulty taking the water chip. Congratulations on solving the first of three major quests in the game. You can now return to Vault 13, finish up any remaining quests there, and talk to the Overseer for a gigantic dose of 7500xp and two new main quests. One of them is to remove the source of the mutant threats, and the other is to kill their leader, both of which you can see on your Pipboy after you receive them.
When you're finished in Necropolis, and after you've been to Vault 13 to pick up your reward, I'd suggest finishing up the quests in The Hub if you haven't yet, beefing up your character even further, make sure that you have 2 Rad-X and 2 Radaway before leaving, and head toward the Glow. Read the beginning of that section before actually setting off.