The main quest basically has the following path:
- Escape Vault 101
- Head to Megaton
- Learn father has gone to GNR
- Go to GNR
- Solve GNR's problems with the satellite dish
- Learn father went to Rivet City
- Go to Rivet City
- Talk to Dr. Li to learn father went to Jefferson memorial
- Go to Jefferson Memorial
- Father isn't there, find note that tells you to go to Vault 112
- Go to Vault 112
- Go into Tranquility Lane, rescue father
- Talk to father, who says we need a GECK to make Project Purity work
- Go to Project Purity (Jefferson Memorial)
- Kill the Super Mutants there
- Do odd jobs for father
- After odd jobs, Enclave invades
- Kill the Enclave soldiers, father kills himself and sabotages Project Purity
- Find Dr. Li and go to Brotherhood of Steel HQ
- Brotherhood of Steel guys tell us where to find a GECK, Vault 87
- Go to Little Lamplight
- Solve Little Lamplight's slaver problems
- Go to Vault 87 and rescue Fawkes, find GECK
- Get kidnapped by the Enclave
- Talk to various people in the Enclave
- Escape the Enclave
- Go to Brotherhood of Steel HQ
- Talk to Elder Lyons and activate Liberty Prime
- Stage assault on Project Purity
- Destroy Enclave and sacrifice self or Sentinel Lyons to activate the purifier
- Why does father go to GNR to talk to Three Dog? What could a scientist possibly want with some stupid radio jockey? Was there absolutely any reason? It's not really on the way to the Jefferson Memorial or Rivet City, so were they just old friends and he wanted to catch up with the guy? And that was important enough to put his amazing incredible project on hold? Or did he know that GNR's dish was broken and that if he stopped by, his son would eventually follow and fix it for Three Dog instead of him? What the heck?
- Father went to Jefferson Memorial and recorded all those audio logs of him talking to himself. Why? Was he bored and lonely? Did he hope someone would find them and hunt him down? If so why didn't he just leave a note, instead of his long-winded ramblings that nobody else wants to hear?
- How did he get into Jefferson Memorial even though it's infested with Super Mutants and hostile auto turrets? I thought father wasn't "much of a fighter" in his words? Did he sneak in? If that's the case why didn't he sneak in later in the game? Wait, so did the Super Mutants know he was there? Were they sent to kill him but arrive too late? Or were they always there? When the Super Mutants learned nobody was there, why didn't they leave? We see they seem to live off of eating human flesh, so if there was no food then why did they bother to fortify and inhabit the place? I'm so foncused.
- So it's implied heavily by the dialogue that Dr. Braun, the guy who is controlling Tranquility Lane at Vault 112, is responsible for creating the GECK. Yet there is no lab in Vault 112, no GECK, no nothing. He doesn't talk about it at all. Was he working on the GECK before the war broke out, but rather than taking the GECK for himself (an amazing piece of technology), he ignored it to become king of a VR simulation? Why? Why didn't he use this amazing technology he built to become king of the real world instead? Does he have ADD?
- So basically the GECK was retconned into being a magic world-creating device that atomizes everything in a radius to create new life. Okay. Uh, so, uh, why isn't there like, a countdown timer on the GECK? Why does the person who uses it immediately die? Wouldn't that be extremely impractical? Can it be remote-opened? Do you use a robot or something? What if you like, drop it, does it go off? Whoops, everyone's dead!
- Anyway, so the GECK was created by Dr. Braun, but he doesn't have one, because... no reason. Instead the GECKs were sent out to various Vaults around the country, even though they were very dangerous and probably should have been entrusted to the military or US government and not just random people. The only GECK on the East Coast, apparently, exists in Vault 87, which is an evil cloning lab... thingy for Super Mutants. Who is creating them there? Nobody. Why are they being created? No reason. But more importantly, why would you put the GECK, aka the [censored] GENESIS DEVICE out of Star Trek III, into a Vault that was centered around doing cloning and sick twisted experiments, and which is so heavily irradiated that anyone but mutants are instantly killed when trying to enter? You're telling me that the GECK is a miracle device designed to save everyone, and someone said "hmm, we've only got a few... put it in Vault 101, the control vault where nothing will go wrong? nah, let's put it in the one with insane hostile deadly mutants and radiation everywhere, that's much safer."
- Speaking of, let's go locate the GECK. We need to use the computer at the Jefferson Memorial. So let's go to the Jefferson Memorial, so we can use the computer. Wait, I thought they wanted to go to the Jefferson Memorial to restart Project Purity? So which is it? Both? Did father lie to us? Whatever. The Enclave invades and father kills himself for his stupid project so we can't learn anything.
- Well, now we're screwed, so what now? Oh, let's escape the Enclave invasion and visit the Brotherhood of Steel! Turns out that they have a computer that tells us where the GECK is. So basically, instead of going to the dangerous Jefferson Memorial and committing suicide, we could have gone to the big fortified Brotherhood of Steel base and just asked them for help instead.
- Wait, come to think of it, couldn't we just have gone back to the Jefferson Memorial and killed all the Enclave soldiers? I mean, we already had to mow down several of them in order to reach the Project Purity control room to witness father killing himself. Why don't we just, like, kill the rest of them, make our stand there? If we can kill a few with no trouble, why can't we kill a few more? Why are we leaving? Why are we giving them time to reinforce and fortify the location? Can't we send one person as an envoy to the Brotherhood of Steel while the rest of us hunker down and keep the bad guys out? At the end of the game we have to use a big giant robot to get past the Enclave defenses, which are only set up because we waited too long to kick them out. I guess all those Brotherhood of Steel soldiers who helped us fight to get to Project Purity again died for nothing/because we were all idiots.
- In Vault 87, we retrieve the GECK with the help of Fawkes. Yay! But then the Enclave knock us out with a magic stun grenade that does not exist anywhere else in the game, and they kidnap us and steal the GECK. Boo! After this, we never see or hear of the GECK ever again. How does the Enclave use the GECK to activate Project Purity? No idea. How did they know how to use it to save Project Purity? No idea. Did Anna Holt tell them, as she admits to blabbing about Project Purity? Maybe, but why would an understudy/lab assistant know a) exactly how Project Purity works, even though she looks too young to have ever worked on it (and I'm pretty sure her backstory says she never did work on it, only with Dr. Li at Rivet City), and b) how would she know how to use this ancient piece of miracle technology to work with another piece of brand-new miracle technology that she shouldn't understand to begin with? Did anyone at Bethesda proofread this or think more than 1 second about it?
- In the Enclave base at Raven Rock, Colonel Autumn interrogates us. If we give him the correct code to Project Purity, we die and lose the game, so we have to lie to him or tell him to piss off. Why does he kill us after helping him? Is he so stupid he concludes that we are no use to him after he got the answer to one question, even though we single-handedly found the GECK, resisted an Enclave attack on the Jefferson Memorial, and did all sorts of other impressive [censored]? Apparently, yes, he is that stupid.
- Fortunately President Eden intervenes and asks us to come speak with him personally. Why? No real reason, except so that we can find out he's actually a computer, which is the most obvious plot twist ever. Wait, if the Enclave are all "humanity first" then why did they assign a computer to be their President? And didn't anyone notice that their President apparently lived for like 200 years? Ah screw it.
- While going to visit Eden, Autumn overrides his orders and tells all the Encalve soldiers to attack us. Why would the Enclave soldiers disregard a direct order from their President, who is also Commander In Chief of their military, for what a simple Colonel says? Wait, so is Autumn like second in command of the Enclave? Pretty sure there are more military ranks above Colonel before you get to Commander In Chief. Does Bethesda not understand how US military ranking works? Did they not just look it up on Wikipedia before hand? Or did they just think Colonel sounded cool and didn't bother changing it to something that made sense? Are Bethesda actually game design and writing geniuses?! I'll let you decide! But the answer is no.
- When we get to Eden, we find out he is a computer (shock!). He tells us that with one simple change, the injection of a strain of FEV into the water filters, Project Purity could be modified to kill all mutated life in the Wasteland. This includes all people, all animals, and probably a good portion of the Enclave too. Let's think about this for just one second. What would killing everyone in the Wasteland accomplish? Isn't this an inefficient plan? Wouldn't everyone shortly realize the water from the big Enclave purifier was not safe to drink, and would just drink other water, like rainwater or toilet water? It'd be radioactive, but at least it wouldn't kill them. Everyone seems to be surviving no problem right now with regular radioactive water anyway, they just need anti-radiation drums/brahmin milk. Wait, why do people drink water when they can just drink brahmin milk, which Moira Brown specifically says can cure radiation sickness? Wait, did you say FEV? Like, the stuff that makes Super Mutants? Why would FEV kill mutants? Wouldn't it just mutate everyone even more? Wait, if you were going to make anti-radiation medicine, why would you start with FEV, aka the stuff that creates mutants in the first place?
- Anyway, it seems like right now Autumn actually has the right idea in staging a coup to overthrow Eden, because Eden is an idiot. This is proven by the fact that it's possible to convince him he is an idiot and that he should die simply by giving him Bambi eyes. Of course, we can never side with him, because the game has designated the new bad guy, whereas Eden, the President of the United States and a supercomputer, is just a miniboss exposition info dump. Why did Bethesda make the President the miniboss and the Colonel, the dude that far outranks him and also seems to be kind of a moron, the real bad guy?
- So now we escape the Enclave base (and meet up with Fawkes on the way, who joins us), which is set to auto destruct. Why is it set to auto destruct? Why would you destroy this incredible repository of technology and science, and kill all these people? How is this in any way productive or useful? Can't we just not blow up the base, and reap all its benefits to advance humanity into a new golden age? I'll bet all this [censored] the Enclave have could be used to solve all sorts of problems. Hunger, disease, hostile mutants... oh right, explosions are cool, forgot.
- When we get out of the Enclave base and return to the Brotherhood of Steel, we learn that Project Purity is seized by the Enclave and that we have to stop them before they press a big red button to turn it on and get clean water for everyone. Remember, Autumn thought that Eden's plan was stupid and just wants to activate the Purifier to get clean water going. First of all, let's ignore the fact that this would all be unnecessary if we had just fought back against the Enclave and fortified the Jefferson Memorial earlier. Autumn is a bad guy because the game says he is a bad guy, but all he wants to do is give clean water to everyone in the Wasteland. Furthermore, unless we were morons, we turned down Eden's offer, so wouldn't that make us a friend of Autumn, because we both want the same thing for everyone?
- The Brotherhood of Steel convince us that the Enclave must be stopped before they activate Project Purity. Why? So the Enclave want to press a button to give everyone clean water, which will instantly cause some sort of problem for everyone in the wasteland? Or do the Brotherhood of Steel just want to be the ones to press the button instead? Why do we have to go fight the Enclave now? Wait, why are the Brotherhood of Steel considered the good guys anyway? All they did was tell us where Vault 87 was and have done absolutely nothing for the people of the wasteland. Meanwhile all the Enclave did was try to get Project Purity back online. Sure, they used a little force to persuade us to help, but maybe they had no other choice given their circumstances. Why can't I join with them again? Is it because they have evil-looking helmets? That means they're bad guys, I guess. Grr, we're gonna get you, rawr! Is this a Scooby Doo cartoon?
- To fight the Enclave and break through the force fields they erected on the road to the Jefferson Memorial in the time we were wasting, the Brotherhood of Steel activate a massive old abandoned US military robot called Liberty Prime, which looks like it's out of an old Transformers cartoon. Where did this robot come from? Where did they find it? Was it already in the Pentagon when they set up their headquarters there, or did they drag it there piece by piece? Why would anyone make such a colossally pointless robot when they could just make a bunch of tanks for far less money and effort? Liberty Prime has a whole bunch of patriotic jingoistic propaganda quotes that he constantly spouts, so are you sure this isn't just some big pro-US military promotional device? And not an armored weapons platform? Which you apparently can't even control properly because it has its own AI? Wait, if the Enclave are the remnants of the US government and Liberty Prime was made by the US government, then why does Liberty Prime fight the Enclave with us? Shouldn't he instantly start killing all the Brotherhood of Steel soldiers and trashing their base? Oh right, he's our friend because just because, stop asking questions damn it.
- So we go to Project Purity, kill Autumn, and then in order to activate it, we have to sacrifice ourselves, Sentinel Lyons, or tell Fawkes to do it because he's immune to radiation. Oh wait, we can't tell Fawkes to do it unless we paid 10 jewgolds, my bad. So uh, exactly why do we have to activate Project Purity now if the chamber is irradiated? Can't we repair the damage from the outside and just wait for it to become safe again? Wait, why is the chamber radioactive? I thought the point of Project Purity was to purify radiation from water, why is it leaking radiation out? Does it have some sort of big tank where it stores radiation, and it has a hole in it? Why would this hole vent directly into the control room of all places, but nowhere else? Did idiots design this device? Wait, so we have enough time to type in the code to activate Project Purity (several seconds at least), but there was far more radiation in Vault 87's GECK room. Why can't we just use RadAway on this radiation like we could in Vault 87? Is this some kind of special radiation that isn't affected by RadAway? Like, microwaves or something? Why would the Project Purity control room be a giant microwave oven? Wait, so even if we sacrifice ourselves to re-activate Project Purity, wouldn't it be kind of pointless to do so if we can't ever access the control room ever again without sacrificing another person? That seems pretty stupid. Wait, so the control room actually keeps the radiation inside from seeping outside. That means that someone must have built the control room to stop radiation from leaking out somehow. So did they know that radiation could leak inside the control room and kill everyone inside? Why did they come up with such an idiotic design? Hold on, wait. Why is there no failsafe? Are you telling me that these people made Project Purity dangerously radioactive, and never built a backup mechanism to shut it down in the clearly foreseen event that it would fail and release deadly radiation upon everyone inside the control room?