All Access Pass: Mothership Zeta (MZAAP)
version 2 (TWO) beta
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Installation
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Install the associated .esp file as with any other plugin.
IMPORTANT: Since this mod goes over a DLC however, you must extract Mothership Zeta from GFWL and place it in Data Files.
Achievements will not be available.
Search PLAYING FALLOUT 3 DLC OFFLINE to learn how to transfer your saves and Data Files.

It *should* be perfectly SAFE to enable this mod before completing the three MZ quests, but as I haven't tested the way it interacts with a runthrough in progress more than once, I don't feel entirely comfortable with making that assurance.

Check it prior if you want to, but since it's not useful anyway until after going through, there's not much reason to have it enabled until after you beat Zeta and the ship is locked off.

Description
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REQUIRES MOTHERSHIP ZETA (PC)

I, like many of you, was somewhat upset with one particular element of the otherwise decent DLC, Mothership Zeta.

This mod fixes Bethesda's strange design decision of making almost all of doors in the Mothership inaccessible after the related quest. An Alien Omnikey is located in the bridge stasis pod to further your exploring and audiolog collection towards Alien Archivist.

This is a quick and dirty fix that should find itself compatible with most mods.
Pretty much every major area on the ship is reopened including the often overlooked Waste Disposal, Engineering Level, and the Space Walk sequence. Yes, you can be beamed up to the Observation Deck again and again.

Best used by characters who have already completed MZ.
You can already have beaten the questline, no need to load an earlier save file.


Use
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After a player completes Mothership Zeta and usurps control over the bridge,
he or she can grab 1 of several Alien Omnikeys lying around. There's one in the Alien Stasis Pod and another underneath one of the staircases next to the observation window. Upon picking up the Alien Omnikey, most of the ship's teleporters, doors, airlocks and forcefields will reopen for your looting pleasure.

You can now backtrack to most every area of the ship so as to recover any unique weapons and captive recordings you might have missed. Beware, however, as some of your alien foes tend to respawn, providing not only an additional source of ammo and weapons but an additional chance at death also...

Areas that should everything work correctly, be at least partially accessible:

Biological Research
Cargo Hold
Cryo Lab
Death Ray Control
Death Ray Hub
Decompression Chamber
Spacewalk
Engine Room
Engineering Core
Experimentation Lab
Hangar
Holding Cells
Living Quarters
Maintenance Level
Observation Deck
Research Lab
Robot Assembly
Steamworks
Waste Disposal
Weapons Lab

Notes / Bugs / Changes

CHANGELOG

Version 2:
Still in "beta", but have hopefully addressed various suggestions without breaking functionality:
Repeating the Spacewalk is less problematic; leaving without "beaming up" will no longer leave you unable to control yourself fully, and a spacesuit will be provided if you don't have one in inventory.
Thanks to 'Wanna be the Guy' for alerting me to what will happen if you didn't miss the Waste Disposal with Sally adventure.
The dummy wall in the "trash cart" is removed and the endcap of that hall will reappear as cleanup from Bethesda simulating an elevator ride. Have got no reports that any area of the ship is still inaccessible yet.
The "problem" door that sometimes gets stuck (Bridge to Engineering Core) has been fitted with additional scripts so that it will open when activated, even IF it says it's INACCESSIBLE or locked.
NOTE:
"ig__" didn't want the Omnikey cluttering up his inventory, so I figured out how to smoothly transition the Omnikey from a Misc. Item to a key so that it is part of the player's handy keychain. Also if a teleporter that you KNOW worked for you before was shut down at the end of the quest, or if you need to activate the Omnikey's powers again, you don't have to drop and pick up the device any longer! Just bring up your Pip-Boy menu (make sure you have the Omnikey) and stubborn teleport pads (Engineering Core -> Observation Deck) will glow to life.

Version 1:

This small modification took longer than expected, and I still cannot guarantee that this mod will work as completely and reliably as it did during my testing, which mainly focused on preventing problems that would occur after the MZ questline. Although this mod shouldn't affect the state of the ship until you acquire the Alien Omnikey, I personally recommend loading it on a completed file. If a door is scripted to relock itself (Waste Disposal comes to mind), drop and pick up the key again. Mothership Zeta's extensive use of scripted doors and events make state changes hard to track.

Tips -

CTD's On Load -
To clarify, I'm guessing this is your problem...
Crashing on loading screen will happen if you're not patched to the highest version or if you're using this mod with LIVE enabled. This mod is only confirmed to work OFFLINE MODE, which means that Zeta must be installed in the Data Files directory as opposed to the LIVE content
directory. The mod will, by virtue of the way the game works, crash if it cannot find the Zeta master file.
Google how to install your DLC in OFFLINE or non-GFWL mode. This will, however, disable achievements. But, you will not have to sign in to Games For Windows Live

INACCESSIBLE ENGINE CORE
To unlock the door to the Engineering Core, you should be carrying the key, as that door is scripted to respond to the presence of the item in player inventory and open when activated.
EVEN if a door appears to be inaccessible or locked, try once anyway with key in hand just to be sure. Doors that do this are that particular door and the Decompression Chamber door.h Dropping and retrieving the key should only be used in the same cell where a door is relocked by script (Waste Disposal when not completed before the end of Among the Stars). If that for some strange reason fails, as it seems to relock, you can always tcl through the door or disable it. But a quick activate should solve.

FUTURE PLANS
As far as Zeta mods are concerned, I'm currently uninterested in making any sort of crew or encounter mods.
DO feel free however to create your own and use this mod to open up the ship. NPC's and dialogue aren't my area of expertise. (May do the Death Ray though...)

Considerations

If you have suggestions for how the process could be improved or problems, PM.
I'm glad to let this plugin be used in a more extensive Zeta overhaul, just contact me first.