I love Fallout 4's story! It has plot holes so big I can fly my vertibird through them!

- If the Institute wanted human specimens unaffected by mutation, why kidnap a baby? Why not invite his parents to move in to the Institute? Why kill off everyone else in Vault 111?

- Why not make Kellogg a ghoul instead? That would have made more sense than the weird cyborg angle.

- Why does the Institute have such a big boner for synths anyway? What are they good for? Do they want to replace humanity or something? Are they good at information processing?

- Why can't I grill Virgil on everything he knows about the Institute, such as its leadership, its motives, its layout, etc? He wants me to steal something from them, after all, so such info would be handy.

- Why does the Institute worry so much about lost synths when they can mass produce them like sausages?

- Why does Preston want me to blow up the Institute? Why not just take over? "Hey guys, my son just named me his successor and he's dying of cancer, so in a week or so I'll be the boss off the place and I can just order them to stop messing with the surface." If they must wreck the place, why not just kill the leadership, enslave the survivors, and seize the technology? Anything would be smarter than creating a radioactive hellhole in the middle of Boston.

- If the Institute's goal is to "rebuild humanity", what have they been doing for the past 200 years?

- It's been 200 years since the bombs fell. Why hasn't humanity started rebuilding? At least pick up a broom and tidy up the place! The game would have made more sense if it was set just five years or so after the bombs fell.

- There's gangster ghoul who locked himself in his basemant and a child ghoul who got locked in a fridge for 200 years. How have they not starved to death? How have they not gone mad?

Here's a lenghty video on FO4's story, seems to be spot on: http://www.youtube.com/watch?v=A34poZ6paGs

Yeah Fallout 4 has the worst Main Story ever.

kidnapping the baby makes the most sense. The older you get, the more corrupted your dna becomes.

Because plot apparently. I agree it makes no sense other than to make the Institute overly-evil.

I guess they (Bethesda) figured the Institute would never work with a ghoul, so they did the cyborg thing.

Well they basically want their own docile workforce and military without having to do any of the menial work themselves. The Institute is basically a scientific utopia where nearly all low-skilled work is done by robots, freeing up the scientists to work and study at their own pace.

Presumably because they represent an intelligence leak as well as a resource-leak. Synths have knowledge of how the Institute works, who's there, and other trade-secrets. So they want to ensure that leak is plugged.

They don't really care about rebuilding the surface, only continuing their amazing scientific advancement in the comfort and safety of the Institute. Their plan is basically to continue to expand their underground dwelling and outlast the surface world, all the while developing marvels of science that, perhaps in the distant future, they can use to recolonize the surface.

1. They had no idea how long it would take to replicate the DNA needed to make synths. In that time Nate and Nora could have died of natural causes, gotten killed, had their DNA messed up somehow, or any number of other problems. Keeping them in the vault, where they would still be viable 100+ years from now, is the better long term option.

2. I would guess they made Kellogg a human so the player is in the dark longer about how long its been. Keeping Kellogg human tricks the player into thinking its been a short amount of time, rather then 60 years. If he was a ghoul, we would know any number of years could have passed, and he would still look the same.

3. Its explained synths don't require food or sleep, not that they CANT eat or sleep, just that they don't need too. Synths can spend 100% of their time working, and having something resembling human intelligence means they can adapt to any job, making them the perfect workforce.

4. Shaun explains they want to recapture lost synths in an effort to lessen the public's negative perception of them, since many rouge synths go crazy and start leading raider gangs and stuff. Though this is largely pointless as they send synths to the surface to collect things, and those synths murder entire settlements in the process.

5. The Institute has to be destroyed because its run by committee. You can't just change it yourself, even if you are named the director, because in most cases, the other department heads can overrule you. Shaun even briefly touches on then when talking about your role as director, every department is largely self sufficient, The Director just moderates were the different departments overlap. You being the director isn't going to lead to any sort of significant changes in how the place works. All the evil stuff they do now will continue on unless its destroyed.

6. The Institute doesn't believe in the people of the surface, they seek to dig deeper underground, away from the world above. They haven't done anything to help the surface because they don't think anything can come of it.

7. They HAVE tried to rebuild. Nick Valentine even mentions that at one point the various settlement tried to come togeather to form the Commonwealth Provisional Government, but The Institue sent synths and killed everyone at the talks, preventing the nation from getting off the ground.

8. Ghouls are healed by radiation. So long as they get exposure to it frequently, any sort of decay from lack of food should be negated. Eddie did have food down in his hideout though, IIRC.

Being self-sufficient doesn't mean the Director can't overrule them or order them about. It just means he doesn't need to micro-manage every decision made.

The Director has the authority to overrule The Directorate. Shaun does so when he names you his successor, silencing protests from the Division Heads, and admonishing them for being insubordinate. In addition, Shaun directly orders the Advanced Systems division to begin the Synth-Shaun project. Despite Dr. Li's belief that doesn't have any sort of significant research value.

He has the authority too, only because they left him.

Do you really think they would let someone who clearly goes against all the ideals they stand for, as a whole, boss them around?

This isn't something that anyone could miss if you paid attention to the story. The Institute constantly mentions replacing people on the surface, infiltrating them, and kidnapping them to be replaced.

They're infiltrators.

They're also vehemently of the opinion Synths aren't human and could never replace humans.

I think people WANT the Institute to be transhumanist but Shaun is disgusted by the very concept.

They try to revolt, actually, and it fails miserably.

Likewise, the Director has control over all the Synths and Coursers.

X6-88 makes it clear their loyalty is to the Director and no Courser will follow a Directorate member over them.

Which is good because it kind of leaves the Institute Directorate up the creek.

We see hundreds of ghouls laying around the places they died. Ghouls go into hibernation if they don't eat or drink.

Gangster Ghoul was in a bomb shelter, though, and still has food.

He was prepared for a LONG stay there.

The dialogue doesn't suggest that. He directly overrules them and calls Justin Ayo insubordinate.

As in any situation, even for a leader with absolute power, revolution or rebellion is always possible. The situation has to be handled gracefully, and gradual changes would be necessary to reform the Institute.

If the Sole Survivor suddenly orders The Institute to become a wasteland cabaret, let anyone in, and boot all the scientists to the surface. Yeah, I imagine they wouldn't take that very kindly.

But the fact remains that The Director isn't a figurehead or only a mediator, he's a executive with definite power to enact decisions, regardless of what the Directorate thinks.

It's a dictatorship, yes.

Agreed.

and again, the Institute's Synths are all programmed to obey the Director with the codes on his office.

Military force all lays with the Director.

X6-88 would put a bullet in the head of the head of the SRD if you asked him.

True, I forgot about that. He's de-factor Command-in-Chief then as well.

Obviously, securing Bioscience and their food supply becomes a top priority thereafter.

90% of these are explained in the game if you pay attention and explore, and the other 10% are explained if you use simple logical deduction.

Yes, but some people need all the information listed in a nice neat menu otherwise the options apparently don't exist at all.