Fallout 3/WMG

The Mysterious Stranger is Satan.
There exists three versions of an unfinished Mark Twain work, which had two different titles. It is called The Mysterious Stranger. The plot is simple: a charming teenager comes up to three boys and claims to be an angel named Satan. He proceeds to show them what a horrible world we live in. It's other title? No. 44. In the Fallout games, The Mysterious Stranger wields a .44 Magnum. Perhaps, in Fallout, God and Satan exist, and Satan Is Good and God Is Evil. After all, we have no idea who started the war. God promised not to flood the Earth in the Bible, but he said nothing about causing humanity to nuke themselves almost to oblivion. So, Satan is pretty much trying to salvage the mess God made and sees that you're the most useful person around. As for the outfit? Well, according to the Bible, angels are pretty freaky looking, so Satan would likely be the same. Trying to make sure not to push you over the edge, he takes on a new look.

G.O.A.T was a satire of the tutorial in The Elder Scrolls games..
Like Morrowind, you're given a 10-question quiz about what you do would do in everyday situations, and this determines some of your skills. But look at what happens in Fallout 3: the students are given results completely contrary to what they thought they were good at, the teacher thinks it's a load of rubbish to the point where he's surprised if you got what you really wanted, and you have the option to cheat on the test. Now consider that this this quiz system vanished in Oblivion and Fallout: New Vegas and probably won't show up in Skyrim, either.
 * Considering that the skill system has been so heavily modified that discrete classes no longer exist, it's a given that it won't exist in Skyrim.
 * Ha. Like classes really existed in Morrowind and Oblivion.

Homosexuality is illegal in Vault 101
Just a thought that occurred while I was reading the Les Yay subtext some people see between Amata and a female LW. The population of the vault is low enough, and dwindling fast, so presumably there would be some sort of enforced programme to ensure continued survival. This extends to others in that they would probably be forced into having children, but it gives any relationship between Fem/LW and Amata an added hint of tragedy.
 * Not to mention the fact that in the Retro-Futuristic 1950's style atmosphere that Fallout evokes, Homosexuality would be seen as a mental illness.

The aliens caused The Great War
One of the tracks on the alien mothership details the mental breaking of a US bigwig who knows the access codes to the nuclear stockpile. The audio cuts out just before he breaks. Given that the aliens have been observing far before 2077, well, maybe they'd gotten enough information on this stage of civilization from our species. "Let's see how they react to near extinction."
 * This is assuming that Mothership Zeta is actually considered to be canon. Every Fallout game (including Fallout 3 prior to Mothership Zeta) has exactly one crashed alien ship. Fallout 1, Fallout 2 and Fallout: New Vegas definitively mark this encounter as non-canon. The Fallout 3 crashed ship is a reference to the same encounter found in both older games. Mothership Zeta adds nothing to the storyline and is never acknowledged by anyone not involved with it, which makes it highly questionable, even for being actually canon in Fallout 3 (let alone the series)
 * The Shi's Emperor indicated the Chinese probably started the nuclear phase of the war, or at least were moving into position to do so when the nukes were launched. Mind, that doesn't rule out alien interference, or that the USA did get in first.

The (Capital Wasteland) Brotherhood's records about the Enclave incident on the West Coast are faulty
The 'Enclave Tactical Assessment' entry in the Citadel's terminals after Project Purity is occupied explicitly identifies the armor used by the Enclave as Advanced Power Armor Mark II, and notes that the Enclave forces are nearly identical to those encountered on the West Coast in 2241. This, of course, makes little sense, as not only does the 'Enclave Power Armor' of Fallout 3 look different from the APA Mk. II of Fallout 2, but it also is nowhere near as powerful as it should be... but it has been more than thirty years since the Oil Rig was destroyed, and even the Capital Wasteland Brotherhood members old enough to remember that time might not actually have seen APA Mk. IIs back then. The records available are probably vague enough that Rothchild and the other Scribes are misled into assuming that the Enclave's matte black power armor is the same matte black power armor as was used back in 2241. As to what it actually is, one theory is that it a power armor designed specifically to be cheap and simple to make - the Enclave has lost most of its resources, and might simply not have the capability to maintain production of APAs, but even relatively weak power armors gives one a great edge over forces lacking power armor...
 * Bethesda overlooked a lot of details from the older games when they made Fallout 3. If they could completely ignore Washington D.C. was leveled and vertibirds used oil based fuel, then confusing mark numbers of power armor is hardly surprising.
 * It goes beyond confusing mark numbers - the APA Mk. I was not matte black, and was superior to every power armor but the Mk. II - but really, this WMG is all about trying to hand wave away at least one of their mistakes.
 * All power armor is weaker than it is supposed to be due to Gameplay and Story Segregation. If it wasn't anyone in power armor would be completely immune to most of the weapons in any Fallout game.
 * The point isn't really that Power Armor is weaker than the fluff says, the point is that Enclave Power Armor is relatively weaker compared to the other power armors than what it is supposed to be - it is barely better than the T-45d, when it should be significantly better than the T-51b.
 * You are comparing numbers of vastly different game mechanics. A large number difference in Fallout 1 and Fallout 2 isn't as significant as fairly minor differences in Fallout 3. The defense numbers were much more important in the first two games because of burst fire, which effectively allowed certain weapons to fire substantially 10-40 rounds, and depending on AP, it wasn't necessarily any slower than firing one round at a time. On the other hand, most of the power armor in Fallout 3 basically put you at the DR cap already, so having more DR on it made little difference. The Enclave armor significantly outclasses T-45d solely because the higher HP is more important overall. The Enclave Tesla and Hellfire armor did also maintain their traditional power armor advantage.
 * Also, T-51b power armor being better in Fallout 3 makes sense. Both sets of T-51b were pre-war, unused suits that were properly stored in sealed bunkers. T-51b armor in other games was armor that has been used for decades and repaired multiple times.
 * The T-51b should still be inferior to newly-constructed suits of armor taking advantage of decades of technological advancement (after all... the Enclave's Power Armors were superior to hardened T-51bs). They are not... at least, if one takes the Brotherhood's analysis at face value (obviously, the point of this WMG is not to). In any case, regardless of attempts to hand wave the power (even if DR gets less important at a certain point, that still doesn't excuse T-51bs having higher DR), there is still the 'does not look like the armor it is supposed to be' thing (New Vegas showed that there was no inherent problem with Gamebryo and models looking much, much more like Fallout 2's Advanced Power Armors). Thus, this WMG providing a hand wave that explains both the power discrepancy (be it smaller or lesser) and the odd appearance.
 * The Remnants armor in New Vegas is still overall inferior to T-51b power armor and even the T-45d is arguably a better overall choice. Despite the slightly higher DT, the bonus attributes on Remnants is worse than T-51b in every category (except Strength where both provide +1) and is extremely fragile. Not fragile for power armor, either. The amount of damage it can take is equal to the most fragile medium armor and quite a few sets of light armor are far more durable.
 * Higher tech does not always mean better in every way. For a very marginal increase in DT, the advances made the Remnants armor worse in every other way compared to T-51b.

Harkness is based on Captain Jack Harkness from Doctor Who and Torchwood.
When Zimmer's android was going to get his facial reconstruction, he found an abandoned U.N.I.T. fort to the north of DC. There he learned about U.N.I.T., the Doctor, and Torchwood, and he decided to have his memories and appearance replaced with those of Captain Jack Harkness. Essentially, even if you restore his memories as an android, he still has the memories of Captain Jack, and also has a desire to reunite with the Doctor. He's also heard rumors of a mysterious alien artifact at the U.N.I.T. fort. It's said to have taken on the form of a British police box.
 * The problem is that beyond the superficial similarity of sharing a fairly common last name, there is absolutely no connection. The entire quest is one gigantic Blade Runner reference and there are absolutely no similarities between Captain Jack Harkness, Harkness, A3-21, or the personality, actions, or memories of either entity.

Bethesda Developers really hate Canada for some reason...

 * In the Fallout back story, Canada is annexed by the United States. In FO 3: Mothership Zeta, you're able to launch a death ray right at what was once Ontario, Canada.
 * Maybe it's because BioWare is based in Canada (Though, not in Ontario).
 * The Canada annexed by the USA thing doesn't prove anything about Bethesda hating Canada: it was established back in Fallout 1.

You died in Vault 101.

 * Amata couldn't get to you in time. The Overseer's guards did and the whole game is a Dying Dream of what could have been...

You never existed in the first place.

 * Alternatively, the entire game is the drug addled fantasy of depressed scientist (James) who couldn't get any action, envisioning himself not only as a Hero who helped save the world, but having a child who would do so as well. His wife dying is a combination of the desire for a co-worker and loathing because she won't look at him.

The Mole Rat is the "invasive animal species" weapon mentioned in a Pentagon computer, and Moira stumbled on the formula for the cleanup agent also mentioned in the same entry.
The little vermin are everywhere it seems, and they die in a spectacular fashion when exposed to the "repellent" that Moira formulated.

East cost super mutants (the yellow ones)will soon die off
After the devastation caused by the combined efforts of the the Lone Wanderer, the Brotherhood Of Steel, Talon Company and Riley's Rangers the population would have taken a serious hit. Add to that the fact they are running out of Forced Evolution Virus and can't breed naturally, they could be wiped out inside a decade.
 * Add to that the Lone Wanderer being fairly likely to get around to telling someone that the East Coast super mutants are Vault 87 super mutants. Much easier to clean out an infestation if you know where it is coming from...
 * The issue is that the Enclave was completely obliterated and the Super Mutants almost completely wiped out before Fallout 3 took place and then they sprang up again, more powerful and better armed than ever before because otherwise Bethesda might have needed to think up a new antagonist group rather then rehashing old ones. Bethesda, for all their merits, has a bad track record of reusing the same antagonists in all of their games, even when they logically should no longer exist. If another game takes place in the Capital Wasteland, it is probably a safe bet that the Enclave and Super Mutants will both be present.

The Lost Hills Elders cut off the Capital Wasteland Brotherhood from reinforcements because they couldn't do much more.

 * The game indicates that the reason for letting Lyons keep his status and rank, but cutting him off from reinforcements were a matter of compromise after no consensus on how fitting his actions were to the Codex could be reached. New Vegas reveals there is a war between the main Brotherhood and the NCR, and although no starting date is given, what we are told means it must have been a while before 2277... quite possibly, before the breach between the Capital Wasteland and main Brotherhood occurred. The Lost Hills Elders might simply not have had the resources to spare to help or punish Lyons (they could have told him he was deposed, but if his subordinates were uncooperative to that demand that wouldn't have done much). So, cut them lose and put off a proper decision until the war is over.

Three Dog is God.

 * Think about it, he always knows every good or bad thing you do without ever leaving his studio. The "Three" in Three Dog is the Holy Trinity, and Dog is "God" spelled backwards. Also, he calls his audience his "children".
 * Was this WMG written before or after the Dead Money DLC came out for Fallout:New Vegas?
 * Plus, he always refers to himself as "your ruler, your master"

Colin Moriarty is only half right about Billy Creel.
Moriarty believes, as indicated by his terminal, that Billy killed Maggie’s parents and the girl as a trophy – but only half of Colin’s musings are true. Billy really murdered Maggie’s parents for supplies (it’s a rough wasteland) but couldn’t bring himself to kill a little girl. . . or leave her to die in the wasteland.
 * The information on the terminal is almost definitely false.
 * There is absolutely no evidence beyond Colin's terminal about Billy killing Maggie's parents, but any NPC that talks about Billy completely contradicts that.
 * Colin Moriarty is a blackmailer and he is probably grasping at straws. Billy mainly worked as a caravan guard until he helped defend Megaton from a bandit raid. Colin also flat out does not like Billy, while everyone else, including Maggie, does.
 * On a meta level, Billy Creel is karmically good.

The Lone Wanderer's mother's (Catherine?) family was involved in the creation of FEV
No real proof but she does seem come from a scientific background (as does James, the Lone Wanderer's dad) so it isn't that hard to imagine she inherited the genes/legacy of the people who made FEV.
 * Might even explain the Lone Wanderer's rather extra ordinary abilities. A little tinkering with the FEV, self experimentation and viola! A Tyke Bomb. Too bad it kills the mother though.
 * The extraordinary abilities could also be explained by every other Bethesda RPG, justified or not, making the PC absurdly overpowered without explanation.
 * That would mean Catherine is well over 200 years old before the game starts. The FEV was developed before the Great War. Even in the sometimes contradictory lore of Fallout 3, the East Coast strain was still developed prior to the Great War.
 * Tinkered with the OP. She inherited the research.
 * The Fallout series has never brought up "genetic memory," so even if she had the genes of the people that developed the FEV, it would be meaningless.
 * There has never been a mention of her ever going to any area where anything related to FEV research is found.
 * The most likely origin for her is being from Vault 101, since that would give the most plausible explanation for how James found the vault, why he went there, and why the isolationist Overseer let him in even though he wasn't originally from the Vault. Otherwise he stumbled blindly through miles of Super Mutant and Raider inhabited terrain, ignoring at least two potential safe havens, and allowed in solely because he was a physician even though he also had massive potential to disrupt the Overseer's plans.
 * If she is from Vault 101 it completely disrupts her ability to have anything to do with the FEV as some sort of "family legacy."