Port with some personal edits of the Lore Friendly Roleplaying rewrite series of mods by MrSwordToast, these mods focus on expanding the choices you can make and rewriting some of the lore to make more sense such as with Megaton and Little Lamplight. Less NPCs that you're forced to kill, and more NPCs that you can kill, the ability to fail some more quests, yay! 

Examples:

-Vault 101-
You can now tell your dad you won't kill the radroach with your BB gun and he'll be proud of you and respect that decision like you'd expect.

It's now possible to kill Amata, Stanley, and everyone else in the Vault while escaping, and lose the ability to ever go back to do Trouble on the Homefront

You can also get through it without killing anyone, the only guard who will attack you is Officer Kendall(You can sneak by him) and the scene with the Overseer and his security is tweaked so that you can go through it without killing anyone.

-Megaton-
Dialogue options to ask why the town was established around a bomb with good justifications, a more sensible reason for tenpenny to want to blow up Megaton and much more lore expanding dialogue choices.

The ability to kill Moriarty without anyone caring, and Gob will take over.

-Vault 112 and Tranquility Lane-
There's like 8 new outcomes for this quest. No seriously it's a ton and Tranquility Lane is perfect now. see the original mod page almost the whole mod is included except for some dialogue that D.I.E.O. also adds and I didn't want these mods to conflict since I use it myself.

Get through Tranquility Lane without even doing Tranquility Lane by breaking into Braun's pod and murdering him complete with a lot of skill checks and interesting writing. 

Kill the robot that gives you the 112 jumpsuit! Yay, murder! 

-Vault 87 and Little Lamplight-
Enter through vault 87 through the actual entrance instead of the post apocalyptic kindergarten, you can still get Fawkes this way.
The gates in Little Lamplight have turrets now to explain how the super mutants or Anakin hasn't been able to get in to kill the younglings yet.

You can open the back gate in Little Lamplight yourself instead of forgetting to talk to Princess and having to run through the caves multiple times.
Notes that attempt to explain why this town is even a thing to begin with.



-Extras-
The ability to fail Replicated Man by killing Zimmer, Pinkerton, or Armitage(who is now a nightmare to fight cause he's a courser from the institute) before the quest is complete.

You can now kill Daniel Little horn and Sonora Cruz, making your bounty perks useless if you wish!

You can now clear the purifier of super mutants without having to kill them for pacifist players.

-Main Quest Endings-
De-linearizes the main questline; Adds three new paths to end the game, two Enclave Paths and Endings, and an Independent path where you destroy the purifier damning the major factions into limbo. 

Rewrites for sending each of your followers into the purifier to make more sense.

You can now kill every single NPC associated with the main quest line with some rare exceptions and still beat the game, even your own dad.

You can also get through every part of the main quest line without killing anyone, too due to how the Enclave have been rewritten.

Far better writing for the Enclave, no longer pure evil for no reason.

This mod is enormous and so will have a lot more compatibility issues that's why I have it as a separate file. 

-Main Quest Endings Lite-

This version of Main Quest Endings has the Enclave content and all rewrites removed for far better compatibility with other mods that do similar things of which there are many, check out the recommended mods for a full suite of mods to bring Fallout 3 closer to New Vegas's style of story telling. Also for people who don't like a more neutral Enclave and want to keep the normal evil Fallout 2 style Enclave. 1/5 of the overall size, and safer to use overall and the story is still completely free form.

You can still effectively do an Enclave playthrough without ever touching the brotherhood due to new changes to the independent path. 

This version is made to be used with other mods such as Functional FEV or Manifest Destiny along with Tweaks for TTW for the best experience. All of your Enclave mods should work just fine with this version.

-Mothership Zeta Enhanced Edition-

This mod completely overhauls Mothership Zeta

Streamlines the main questline and makes half the DLC optional content, the followers in the DLC will now follow you regardless of where as long as it's in the DLC

You can now explore the ship after beating the DLC

Toshiro Kage has far more going on and you can speak to him in Japanese with a very high INT check

More lore explanations

More skill checks to bypass certain parts of the DLC such as the ending boss fight and getting out of the holding cell

Adds DLC rewards at the end

Makes starting the DLC optional to get the Alien Blaster

and more, this one is pretty damn big and complicated too see the original mod's description for more info.  CURRENTLY UNTESTED
Definitely not compatible with your Mothership Zeta mods, and no compatibility with Delay DLC Redux, I'm not too interested in maintaining this full version so others can make patches for it unless I get the motivation.

-Mothership Zeta Enhanced Edition Lite-
This version is also untested but doesn't touch anything that can break level progression so it's safe.
This is more of a personal version and cuts out the majority of the changes in the original for far better compatibility and simplicity while keeping what are in my opinion the most important changes
What remains:
Pretty much any new content has been kept with any edits to vanilla content removed unless it's high compatibility.
All of Toshiro Kage's changes
Some notes.
More skill checks to bypass certain parts of the DLC such as the ending boss fight and getting out of the holding cell.

There are other mods that do the rest of what the original mod does so I will likely be supporting this version more than the original.
Check out Mothership Zeta Rehaul for that, I have yet to look into it's compatibility though.


For more info please visit the original mod pages:

Vault 87 and  Little Lamplight

Megaton

Vault 112 and Tranquility Lane

Vault 101

Main Quest Endings

Mothership Zeta



Compatibility:
This mod edits the main quest line and may break if other mods edit the same main quests and or their scripts. Also essential flags will not be removed on NPCs that are overwriting it, basic XEdit knowledge is useful to fix that, if you have a mod that overwrites a script or quest from this mod ask in the comments for a patch and I'll see if I can make one.  3DNPCs TTW needs to be loaded before MQE or else MQE will break.



Some content from the original mods had to be removed or I removed them for design choices, usually because other mods handled them like D.I.E.O., for compatibility reasons (Megaton Jail, some Dialogue Choices), or I just couldn't get it to work like telling Amata to distract Kendall.
Any content from the base game that was removed from the original Rewrite mods has been restored, being a baby is no longer skipped at the start of your playthrough, 
I for one like the tedium of being a child that is likely quirky as hell from your sprinting and visible first person model mods.


Recommended mods:

Functional FEV --- HIGHLY RECOMMENDED --- Adds a post game world for an Enclave FEV path so you don't feel like you're missing out on Broken Steel as much. MQE full needs a patch in the misc files and there's one for the Lite version too to get rid of an unnecessary popup. 

TTW (D.I.E.O.) Dialogue and Interactions Expansion Overhaul  --- better and more dialogue options, no patch needed, very minor change to some player prompts depending on which mod overwrites the other. Make sure Main Quest Endings overwrites this mod just in case.

True Open World DC --- Unexpectedly compatible! Just make sure True Open World DC Overwrites this mod and that you get the patch in the miscellaneous files so you can enter Vault 87 through the main entrance. Not compatible with Main Quest Endings.

Tweaks for TTW --- slaves in major cities, enclave ceasefire, a lot of world-building options. Make sure to check out all the options and configure them.

Farms of the Capital Wasteland --- no more starving towns.

DC NPCs TTW --- It's like The Living Desert but for Fallout 3, adds more reactivity to the world and should work without a patch but I will look into it at some time to make sure.

Raiders of the Capital Wasteland --- fleshes out raiders a bit more, adds a few types that inhabit their own areas, and lets you become a raider even.

Essential to Protected --- Kill essential NPCs to get around having to have patches for NPC mods, and break the game in new and unique ways! They won't die if a Deathclaw decides your dad looks like a good snack, only if you kill them yourself.

Ties That Bind --- You get an Australian sister somehow, woo! make sure Lore Friendly Roleplaying overwrites Ties That Bind and that you are using JD's version specifically. Not compatible with the full Main Quest Endings

Father's Fallout --- Makes dad get really really mad at you if you tell him you blew up Megaton, don't use with the full Main Quest Endings, there's already something similar included.

Useful Megaton Purifier (TTW) --- Lets you use Megaton's purifier after helping them out.

Manifest Destiny --- Adds an Enclave post end game kind of like Broken Steel, not compatible with full Main Quest Endings, make sure this overwrites Manifest Destiny.

TTW New Vegas Speech Checks --- Very minor conflicts as long as you make sure MQE loads after this; this mod should load pretty high anyway.

TTW Reputations  --- Same as above.

Known Issues:
Don't go into Little Lamplight from inside of Vault 87 if you didn't get access yet unless you wanna have a weird talk with McCready.

After beating the game as anyone other than the BOS going into the LAB will disable your ability to take out guns while you're there, use enableplayercontrols in console to fix. I can't find which script, quest or whatever is causing this so I can't fix it internally yet.

The brotherhood can have some issues with hostility as in when you're supposed to be hostile to them, sometimes there's a few that are not, still not sure why but it's rarer now.

Although all speech checks work just fine, they do not use New Vegas's system exactly so there are minor inconsistencies. I want to change this sometime but it's really minor and I'm really lazy.

This mod doesn't use AI Voice acting which may be a plus or a minus depending on the player's point of view instead much of the dialogue isn't voiced or is voiced by real people who have given it their best shot. If it's too jarring to hear a characters voice suddenly change you can safely delete the Voice BSA in the files after installing.