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Here is another optional area that's great for some extra weapons and ammo (from the Gun Runners), quests and especially to upgrade your plasma rifle and power armor. I'd recommend that you wait to come here until finishing the Brotherhood of Steel, as you're nearly in the end game, if not there already if you have been following the walkthrough. The Boneyard is simply the place to prepare you for the two remaining and required areas of the game, the Military Base and Cathedral.
Its southern and main area is called Adytum, so if you see reference to that name throughout the game, that is essentially the Boneyard inner city. To its north is the Downtown hub, where the Blades (they're good) gang is. To Downtown's west is the Library and to its east is the Warehouse (where deathclaws be). To the Warehouse's east are the Gun Runners.
Adytum: the first place you enter. The Boneyard inner city
Downtown: the hub of the Boneyard and location of the Blades gang
Library: an NPC, Katja is stationed here, at the Followers of the Apocalypse
Warehouse: a small area in between Downtown and the Fortress, where deathclaws are
Fortress: home of the Gun Runners, where you can buy nice ammo and weapons
Here is a list of the significant quests in the Boneyard, 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.
Raise Your Luck:
In a tent on the east side of Adytum you'll find Chuck, the tarot card reader. Save your game, and continue asking for readings until the Fool card comes up. You'll get a permanent +1 increase to your luck. It is not necessary to reload your game unless you do something wrong, like make fun of him. You can continue to talk to him and ask again for a tarot reading until the Fool comes up.
Upgrade Your Equipment:
In southwestern Adytum, find Miles the chemist and speak with him. He'll ask that you deliver hydroponic parts to Smitty for him. Agree, and travel to the Warehouse area east of Downtown. The area has up to 3 deathclaws so be careful. The parts are on the east side of the building, so when you have them, bring them back to Miles and he'll ask that you deliver them to Smitty (in an eastside buliding of Adytum). When you do, you'll receive several stimpaks and 250 caps. Most importantly, you'll now be able to upgrade your Plasma Rifle and Power Armor. If you have the Plasma Rifle, he'll trade it in for a Turbo Plasma Rifle, the most powerful weapon in the game (in my opinion).
Likewise, if you have the Power Armor, Smitty will request that you run to The Hub and pick him up a set of Chemistry Journals. You'll find them at the library in Downtown. Ask Mrs. Stapleton for them, and she'll hand them over for 750 caps. Bring them back to Smitty (they look like a Big Book of Science) and he'll upgrade your power armor to Hardened Power Armor, the most protective suit of armor in the game.
Recruit an NPC, Katja:
On the Library map, west of Downtown, you'll find appropriately enough, the library. Inside, you'll find Katja. Tell her you're in town briefly yourself and she will join you for 200xp.
The Regulators vs. the Blades:
When you talk with Zimmerman, the mayor of the town in the west building of Adytum, he'll ask that you kill the leader of the Blades, known as Razor. Head north to the Downtown area, enter the Blades building and you'll find Razor in the southeast room. Instead of killing her, give her a chance to explain... and you'll find that the Regulators are really the "bad" guys. She'll even give you a holodisc as evidence of their brutality.
You can then ask Razor what they'd need against the Regulators and she'll tell you weapons. Fortunately, the Gun Runners have a supply of them if you can convince them to lend them to the Blades first.
East of Downtown is the Warehouse area, and a dangerous place if you're ill prepared. Roaming the surface of this small area are usually a few deathclaws, worth 1k xp each if you defeat them. Either take them out on your way to the Gun Runners or try and make it to the east end exit grid. These deathclaws is the single-most easiest way to earn experience in the game, provided you are properly equipped. When you kill the deathclaws in the warehouse area, if you wait an hour, leave and return, they will respawn. You can do this as many times as you please. Only when you kill the mother deathclaw downstairs from the Warehouse will they stop respawning. Be sure and grab the hydroponic parts on the eastern end of the building if you haven't yet for the Miles quest (above).
When you've reached the Fortress area to the east of the Warehouse, there will be a giant radioactive moat around the Gun Runners building and a guard at the southern narrow land bridge. Tell him you'd like to trade and he should let you by peacefully. Inside the building, speak with Gabriel and he will ask that you take care of the deathclaws if you want any help from the Gun Runners. So head back to the Warehouse map, take care of the deathclaws on the surface, and then take the stairs inside the shell of a building to where the mother awaits. The mother is fairly tough, but you should be able to handle her by this point. Don't forget to break the eggs down there for a nice 5xp each on your way out.
When you're done with the deathclaws, return to Gabriel for 1000xp and the ability to ask him to help the Blades with weapons (if you've previously spoken with Razor). In addition, you'll have earned yourself a 20% discount with Zack the merchant if you've helped the Blades, though you still get a discount if you helped them with the deathclaws. Take advantage of Zack, as not only does he carry a lot of useful energy ammo and a plasma rifle, but he replenishes his money every time you speak with him, giving you a virtually unlimited amount of caps for turning in loot.
Return to Razor of the Blades, and tell her you've secured her weapons. She'll now ask if you want to help them get rid of the Regulators. Agree and you'll be taken to Adytum for a large-scale battle. Beware that Miles and Smitty can be killed in this battle, so either make an effort to protect them or be sure to have upgraded your plasma rifle and power armor by this point. Save prior to the battle to avoid any misfortunes.