So, the Entire Plot was *FULL* of "Wait..... what?" Moments...
So you start this game, go through a fantastic character creation and development sequence, and bam, the plot starts with a bang! Before we know it we've got our first major plot twist, that your father (and mother) were originally from outside the Vault.
...wait..... what?
I love a good plot twist as much as anyone (and then some), but outsiders can't just move into a sealed community without anyone and everyone noticing. At any rate, supposing that everyone in Vault 101 besides the overseer is a moron, we venture out to find dad. We visit Megaton, think it's a neat concept as we save or destroy it, and move on to Dad's next place of interest. We finally uncover Dad's driving motivation for leaving the Vault and starting your quest: He's trying to build a water purifier.
...wait..... what?
A water purifier? Really? I can obviously see how it might be important to the survivors in the wastelands, but it's not exactly the epic destiny or back-story I imagined that daddy might have. I mean, we've got mutants, warring fractions, and plenty of other sources of radiations... as wonderful as it would be for the water basin to be purified, it seems like humanity has more than enough other problems on its hand to make such a big deal about clean water.
Whatever, we'll run with it. So, we run off and find out that Dad's stuck in the Matrix, or at least Pleasantville. The "Good Karma" thing to do is to use the failsafe terminal to start a communist invasion that kills all the happy citizens in a sudden and terrorizing death.
...wait..... what?
Yeah, they were brainwashed... there were also happy. And, not dead.
At any rate, me and dad are free now, and he won't stop talking about his bloody water purifier. Great. He explains how the project was threatened after an army of super mutants took over the area, and convinces everyone to get the band back together. They walk over to Jefferson Memorial, and calmly wait for me to go kill all the super mutants.
...wait..... what?
This army of super mutants drove out an entire team of people, and you want me to show up 19 years later and kill them all without any help? Either everyone involved is a pansy, or they assume that I'm the Juggernaut. Whatever; I kill all the mutants with the magic of my quickload perk (All hits are critical! You never miss!) and get dad back in. Dad has me do some really trivial and boring fetch quests in the basement, which are apparently too difficult for anyone else based on his constant praise at how excellent I was at flipping that switch. Of course, this is all just an excuse for the plot to get me in the best seat to observe the Enclave invasion.
...wait..... what?
Why is the shadow government invading our water purifier?
I am expecting some dumb monologue from a villain any second now, about how "The Enclave needs people to need the Enclave" and how purifying the water would somehow lessen the power they hold... or something. Sure enough, I get up there to see some Liquid Snake wanna-be (with the wrong accent) saying that the government is taking over the project so they can activate it.
...wait..... what?
Isn't that what we are going to do anyway? Activate it and purify the water? Why did you need to invade the place guns-a-blazing? Dad firmly tells the people with guns to take a hike, so that he can activate it and purify the water.
...wait..... what?
Dad, why are you arguing with someone who is telling you at gunpoint to do what you want to do anyway?!?! WHY IS ANYONE EVEN FIGHTING AT ALL, WE ALL WANT THE SAME--OMG HE JUST SHOT HER WTF IS GOING ON AHHHHHHHHHH!!!
Then Dad for some reason causes an explosion, killing everyone inside the chamber.
...wait..... what?
Now we have to escape through the secret passageway!
...wait.... what?
Your water purifier has an extensive secret tunnel system leading to the Brotherhood of Steel headquarters??? Why is the Enclave even chasing us?!? I'm still have no idea why we are fighting over a water purifier we all want activated in the first place; I'm expecting any moment for someone to jump out and reveal that it's actually a water *CANNON* or some other amazing military weapon and me go "Oh, okay."
Meanwhile, everyone is still obsessed with activating the purifier. Um, guys? I appreciate the work ethic, but THE GOVERNMENT JUST INVADED AND KILLED HALF OF US. Apparently the missing piece is a GECK. Wait, that's it? All this time, the only missing thing was a GECK? They don't exactly grow on people, but it's been like two decades people, sheesh! If this water purifier is so amazingly important... nevermind, screw everyone, I'll go get your stupid GECK. So my new radiation-proof pal Fawkes gets the GECK for me, and the Enclave shows up to steal it.
...wait..... what?
The Enclave has an army. They control the Vault system more than anyone, why the heck did they need ME to get them a GECK? Villains are supposed to manipulate the heroes into doing stuff they themselves CAN'T do! Also, pardon me Colonel Throwaway-Villain, but aren't you supposed to be dead? Whatever, Eden is calling me up to his office, and the Colonel orders his men to kill me anyway.
...wait..... what?
I thought he was keeping me alive to get information like the access code... or something. (Why the heck does a water purifier need an access code?!?) Now suddenly the President wants to meet with me... and that is so terrible that you immediately rebel against him and order all the soldiers to kill me? So I make it to Eden, oh ho ho, it's a computer. Eden tempts me with its evil plan to inject a solution that will use the purifier to demutate the wasteland.
...wait..... what?
How is the evil? Sure, it's not the most compassionate solution, since it kills most of the currently living people, but it also ACTUALLY gives the future a world without mutants, radiation, and constant war! (Instead of "Oh, well everything still sucks, but we've got cleaner water!") Given that the theme of Fallout 3's plot is "sacrifice", how is sacrificing current humanity for future humanity the "worst" or "most evil" option?
Anyway, I say "No, I'm not going to do your dirty work Eden, now would you kindly commit suicide and self-destruct the base?"
Eden: "k"
...wait..... what?
I get back to the Brotherhood with my boy Fawkes, and tell them the news: The Enclave stole the GECK! They might activate the water purifier, oh noes!
...wait..... what?
Why do we care if they finish the project and purify the water? Isn't that what we want? Doesn't it seem--you know what, nevermind, we've been here before.
So we invade with an awesome robot and fight our way to the purifier. Liquid Snake tries to stop us from... whatever it is we are trying to do. (Stop them from purifying the water, so we can purify the water?) Fawkes kills everyone who looks at me funny, and we go up to the controls. Oh noes, the Enclave sabotaged it so it is building up pressure and will explode!
...wait..... what?
So, lemme get this straight. After all that trash-talk, they actually predicted all along that we'd kill them... so instead of purifying the water like EVERYONE wants, they decided they would rather make it explode to take us with them?
That's just stupid.
So, someone has to go inside to put in that stupid activation code that will magically purify the water and stop the impending explosion. Problem is, for some reason or another it's radioactive, so going in will kill you.
...wait..... what?
I've got like a zillion Rad-Xs and Radaways and Radiation Suits and who knows what else to fight radiation guys. I've been doing it the entire game. I don't care how super radioactive it is, I only have to hit FOUR BUTTONS, sheesh. Whatever, I'll just have Fawkes do it. The game even let's me ask him: "This is your destiny, my friend. I cannot interfere."
...wait.....
...wait.....
...wait..... WHAT?!?
Why on earth does me or the cardboard-cutout military daughter have to die, when Mr. Invinci-pants could just do it? Pushing FOUR BUTTONS isn't that hard... I know you are upset after you were rejected at Gears of War 2 enemy castings Fawkes, but that's no reason to make the playable character die! What's that, you want me to follow in my father's footsteps as a metaphor? Screw that, what kind of person kills someone just to be poetic? For crying out loud, dad's body isn't even there anymore!
Fallout 3 had excellent writing, settings, voice acting, presentation, and characters... BUT THE PLOT MADE NO SENSE. Go tell your friends that you just played a game where the premise was: "Two sides in an apocalyptic future fight to see who can turn on a water purifier first!" They will probably respond:
...wait..... what?
Subject: Fallout 3 Plot Analysis (by Officer Cooper of GameFAQs) 
Sun Nov 30, 2008 4:12 am
Sweetness. 
Now to turn on that water purifier. 
