This quest is a bit difficult to figure out, but it isn't impossible. If you don't want to be hassled with the quest, here's what you do:
1. Open the console, click on the front door and type in "unlock"
2. Open the console, click on the generator, type in "set GeneratorRepaired to 1" and then start it up
3. Open the console, click on the filtration system, type in "set FiltrationRepaired to 1" and activate it



Pre-War Shelter 2.0 - By Crotalus
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Description:

This plugin adds a pre-war shelter on the river shore above Megaton. The shelter is moderately sized with a laboratory, bedroom, and kitchen. There is also a separate underground cistern attached to the shelter. Full functionality of the shelter must be restored by the player through a small mini-quest.

Special Devices:
Cook-o-Matic Oven - Capable of cooking five different meals
Incinerator Unit - Stores trash and can incinerate instantly
Minifacturing Machine - Repairs weapons and presses ammunition
Radiation Scrubber - Removes one-half radiation level once per day
Research Terminal - Raises skills points with scavenged ruined books
Small Fruit Tree - Bears special crippled limbs healing fruits
Water Purifier - Simple device to purify all your dirty water

Scripted Features:
Eight Light Switches - Functional light switch for every room
Central Filtration System - Controls water flow in the shelter
Central Generator Control - Controls power to devices in the shelter
Vestibule Security System - Decontamination spray and locking blast door

Miscellaneous Features:
A mini-quest to restore functionality to shelter
Actor furniture/interaction markers (for companions)
New containers and encounter zone (for compatibility)
Full Room marker and portal optimization
Full interior and exterior NavMeshing

This is the first real mod I've released; making the entire mod was a learning process. I've tried to make this mod as professional as possible; there should be absolutely no conflicts or dirty forms if I did everything right. Any comments and suggestions are encouraged as well as any bug reports or problems.
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FAQ:

Q: Where is the Pre-War Shelter?
A: The shelter is north of Megaton; it has its own map marker.

Q: I need help with the mini-quest.
A: Look in the hints section below.

Q: How do I access the Underground Cistern?
A: Look in the hints section below.

Q: Why won't my books work with the Research Terminal?
A: The terminal only salvages "ruined" small and large books.
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Installation:

1. Extract the Data folder into your Fallout 3/Data folder.
2. On the launch menu, go to Data Files and check Pre-War Shelter.esp

Although new versions should always be replaceable over old versions, it is nevertheless a good idea to do a thorough check before saving with the new version in case any unexpected problems do show up.
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Uninstall:

1. Remove Pre-War Shelter.esp from your Fallout 3/Data folder.
2. Remove the Crotalus folder (located in the Meshes folder).
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Compatibility:

This plugin only uses existing Bethesda art assets; plugin will be affected by texture or model replacements that change the original art assets. Plugin specific containers and a "no-respawn" encounter zone are used to guarantee against compatibility problems with other plugins that might edit original container properties, such as overhaul mods.
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Thanks To:

Bethesda for the GECK.
Akallabeth, CNIall, F1 GTR, pintocat, StVladd, and WillieSea for ideas and help.
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Licensing:

Do whatever you like, short of releasing this file under a different author. If you need help understanding the scripts, don't be afraid to message me.
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Changelog:

1.2 to 2.0
- Added Underground Cistern cell space.
- Added some more display and storage space.
- Added five completely new special devices.
- Added Filtration System and Generator Control interactivity.
- Added mini-quest to restore full functionality to the shelter.
- Added one more meal option, Mirelurk Meal, to Cook-o-Matic oven.
- Added ammunition pressing functionality to Minifacturing Machine.
- Added automatic decontamination spray to vestibule chamber.
- Extensive changes to the lighting system in the shelter.

1.1 to 1.2
- Added a small vestibule to smooth transition from the cave to the shelter.
- Fixed a minor problem with minifacturing machine not displaying repair option.

1.0 to 1.1
- Added a separate acoustic space to the cave area to distinguish from the living area.
- Added more effects to the living area and cave area to give the place more "movement."
- Changed the front door into an automatic door that closes four seconds after opening.
- Added Minifacturing Machine and light switches.
- Added miscellaneous statics to take up space.
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Hints:

Shelter Access Key - Will is going to Georgetown. What is the name of Fallout 3's grocery chain?
Generator Fuses - They are located inside an isolated closet, next to a bottle of Nuka-Cola Quantum.
Filtration Cartridge - Tom wanted to meet Will at certain city; what happened to the city's name?
Underground Cistern - The passcard/key is sitting out in the open in one of the lower level rooms.