A few theories after listening to some people.

[SirTwist]

I have played through the game fairly far in a few playthroughs. While playing, I discovered a couple people who presented some lore, etc. to the game that I enjoyed bits and pieces of. I had to stop watching them after a while, as they kept going further and further out into left field. Allow me to ask a question here. When you encounter Father, who do think this person is? And who do you think the child is that accompanies Kellogg, in his memories, and is at the Institute? The reason I am posting this here, rather than make a video, etc. is because I would rather type than talk all this out. And also provide some place to discuss things, rather than read comments on a video. Here are my guesses as to identities of people in the game, as well as some speculation on things. The only evidence on the timing is by known manipulators and even liars. And there is no proof as time, other than what you are told. I believe that "Father" is not Shaun. There is zero proof of this. If he has a genetic disease, that either parent may have had before the war, they would have had anti-bodies that could be extracted to cure Shaun, and keep him alive, if he is that old. However, this does not happen. Since the two people who tell you most about Shaun do lie to you, they aren't to be trusted at all. I believe that "Father" is an honorific given to the man who is appointed director of the Institute. Mother would be the female director. Overall director that is. I believe the the child you see in Kellogg's memories, and you meet in the Institute when you first enter, are one in the same. Given 10 years, the Institute can provide post-hypnotic training, programming, etc. to a child who can be made to believe he is a synth, rather than a human being. I will dive more into things in a moment. The only proof we are given is not some log, or computer entry, or anything else. It is word of mouth. And me, I don't believe any of it. I am not done, but I will make some points, below, as to my reasoning. I do know some about genetic cloning, etc. I won't use big terms, etc. However, I do want to state that I have done some looking into things, and also thanks to internet, movies, etc. a bit about cloning. Not a ton, mind you, but enough to support some points.

 

1) The institute, from the start was involved in many different experiments, even before the bombs fell. However, everything halted when that happened, as they needed to save themselves, projects, etc. They did what they could.

2) The Institute went underground, with early passages to the surface to get readings, etc. of outside conditions. They are fairly genetically diversified, as well as able to have children, etc.

3) After some time, the radiation was infiltrating into upper passages of the Institute, so they had to go down further and further. To the point where they are now.

4) The time, etc. to get that far, as well as several attempts at a variety of things, were a hindrance to one of their main projects, human cloning. They were stopped because of a few problems.

5) The gene pool was limited, as well as contaminated by radiation. Not enough to cause major problems, but enough to start the ball rolling.

6) Also, there weren't enough "clean" stem cells to clone humans.

7) While digging, surviving, etc. the Institute find out about Vault 111, through the security and lab staff that were stationed there. However, did not have the means to get in or out easily enough, at the start.

8.)I wasn't until they were at their current level of technology, as well as power levels, before they could do what they needed to, to get in and out, without all the problems that the staff had getting out of Vault 111.

9) Kellogg and crew were the first people in the vault since the staff left. The dialogue that Kellogg has with the scientist is that the Old Man wants the baby, by any means necessary. And to keep alive one of the parents.

10) The "Old Man" is Father, see above. And is NOT Shaun. Nor could this person be Shaun, at all.

11) The Father we meet is not Shaun, because he would look enough like both parents to recognizable at any age. However, Father doesn't look like either one.

12) At some point, Father tells us that he is dying of a disease. It has to either be a genetic disease, or cancer. My bet is on some sort of genetic disease that is not from the PC, or the spouse. Rather, it is from the limited gene pool I mentioned above, and can be also the result of cloning genetic material that is not exactly stable. And he would have asked us to give a sample of DNA, and compare to his, to see if there is a cure. Since that has not happened, leads me to speculate on things,

13) If the Institute wanted Gen 3 synths to look as human as possible, they would want a variety of people, that were from pre-war, not just one baby, and it's parent. However, there would be some problems with moving the pods, etc. elsewhere. But it could have just taken a pair out at a time, and allowed to have children, and use some stem cells from them, and grow their own synths. However, this is not the case. They stole one child, and that is supposed to be the base for Gen 3 synths? Nope, not in my book. My book says that they had Gen 3 synths before this, but wanted to extend their life, as well as fix some problems. And that comes from fresh stem cells. And to get fresh stem cells, they killed the spouse to get the baby.

14) They ended up fixing some Gen 3's, even created ones, thanks to the baby. However, they will need more, so you are it.

15) 10 years, not 60, pass, and you are released. I don't care what the game claims, nor what others claim. It is 10 years, not 60. The time doesn't mesh up. And also, remember there are liars and manipulators operating.

 

I know this is long, but I am pretty sure I covered enough to at least support some things, and maybe put some new spin on things. And since there is very little to no evidence, I believe that Father is NOT Shaun, and that the child is actually Shaun.

[Roentgens]

Father is Shaun. If you change your character's face, Father's face will change along with it. If you look at two different playthroughs, with different looking characters, Father will not appear the same. Sometimes it really is just that simple, and we have to use Occam's razor.

 

The mystery isn't Father's identity, but rather his motivations.

[TheGadget1945]

When you think of the quantity of material which would be excavated to build the Institute , I would like to know "where did it all go ?".

And why, when both the Railroad and the Minutemen found the sewer entrance to the Institute on the holotape scan, didn't Proctor Quinlan find it ?

[MightyZ0G]

very interesting points. I never believed that Father was Shaun. it is implied that Father orchestrated your release from vault 111, so why didn't Father send a Courser and a few gen 1s to rescue you and take you straight to the Institute? why did he just unfreeze you and leave you to your own devices in a world over-run with raiders and super-mutants (as well as mutated, dangerous wildlife), new diseases and lethal radiation storms?

but if Father IS telling the truth, why are all the synths hostile to you the instant they see you? you don't have to do anything yet the synths attack you on site.

it's only when you have killed Kellog and a courser and infiltrated the Institute that Father plays on your emotions, after messing with your head 1 last time by having the synth Shaun react with fear at the sight of you and then call someone else father.

if Father really is Shaun, why is he punishing you?

[SirTwist]

Roentgens, nice name by the way, the only empirical proof that Shaun is Father is him saying so. That is not proof. And 98% of the Commonwealth have one feature, or another that looks like what you drew up on both parents. But you aren't their parents. I digress, though. Again, it's not defined as to whom Father is, aside from him telling who he maybe. As I have stated, the possibility of him looking like his "parents" is because he is a clone of Shaun. Not a synth in the traditional sense, but a clone nonetheless. It is speculated that he is your son. But not proven beyond a reasonable doubt. And I doubt that man more than 90% of everyone else in the game, including Kellogg.

 

TheGadget1945, I believe a few things happened to it. One is that some of it was dumped elsewhere. Some of the more stable, etc., material went into shoring up things so that other material was stable. And even in building. As to Proctor Quinlan, I believe he is more of a historian than anything else, and he is more concern with overall technology than with with finding the Institute. However, it could be something that doesn't cross his mind, a whole lot. I believe the Minutemen and Railroad have a more vested interest in getting to the Institute, and saving people/synths, than the BoS. The BoS, under Elder Maxson, doesn't want the tech of the Institute, but wants the source destroyed. And with the source destroyed, the tech will disappear. I don't care for him as a leader. I don't fully trust his motivations, either. I believe he wants all tech under his purview, and wants it bottled so that no one goes beyond certain levels, so that the Great War doesn't happen again. I may do some stuff on him at another time.

 

Mighty zog, thank you for this. I believe that you have answered some potential problems with my theory about the whole Father/Shaun thing. Why not save both parents, and not just one? Unless they have someone else who can also assist in reproducing untainted stem cells. However, I believe some of the questions you asked were answered. The one about leaving you to your own devices is to test you, and see your reactions to situations. I believe that Father is not punishing you. I believe that Father is trying to mess with your head so that you don't know what is true or not. I have never trusted that man even the first time I met him. I wanted to blow his head off, and even kill the boy. Then tear through the Institute, looking for answers. And real, solid, empirical answers, not the ones we have. I find myself still wondering about the motivations of Father, and what he really wants.

[MightyZ0G]

but why test you? Father knows you didn't abandon him, you shouldn't have to prove anything to him.

my theory is that Deacon released you from the vault because he wanted a loose cannon going after the institute and that's when Kellog went into hiding. then the institute send gen 1s out to stop you after they realise that the wasteland won't stop you.

if it was a test, why didn't Kellogg say "congratulations, you've passed" instead of forcing a showdown?

everything Father does is an attempt on your life until you come face to face with him and to me it looks like a "well that didn't work, let's try something else" situation using mind tricks and playing on your emotions rather than anything else.

this fits if Father is The Old Man that Kellogg refers to in the vault.

another problem with the timeline is that Kellogg would have left Diamond City recently after the courser took Shaun back to the Institute or his trail would have been too old for Dogmeat to follow and Ellie would not have remembered him living there if it had been that long ago.

the other problem with the "test" theory is that even if you pass, you get exposed to radiation. that would render your DNA as useless to the Institute as the DNA of every raider and scavver. it doesn't make sense for Shaun to do that if he is Father and wants you to carry on his work.

 

 

whatever the truth, I love the way Bethesda leave room for each player to have their own theories and how any of them could fit into the canon (although not all at the same time)

[TheGadget1945]

but why test you? Father knows you didn't abandon him, you shouldn't have to prove anything to him.

my theory is that Deacon released you from the vault because he wanted a loose cannon going after the institute and that's when Kellog went into hiding. then the institute send gen 1s out to stop you after they realise that the wasteland won't stop you.

if it was a test, why didn't Kellogg say "congratulations, you've passed" instead of forcing a showdown?

everything Father does is an attempt on your life until you come face to face with him and to me it looks like a "well that didn't work, let's try something else" situation using mind tricks and playing on your emotions rather than anything else.

this fits if Father is The Old Man that Kellogg refers to in the vault.

another problem with the timeline is that Kellogg would have left Diamond City recently after the courser took Shaun back to the Institute or his trail would have been too old for Dogmeat to follow and Ellie would not have remembered him living there if it had been that long ago.

the other problem with the "test" theory is that even if you pass, you get exposed to radiation. that would render your DNA as useless to the Institute as the DNA of every raider and scavver. it doesn't make sense for Shaun to do that if he is Father and wants you to carry on his work.

 

 

whatever the truth, I love the way Bethesda leave room for each player to have their own theories and how any of them could fit into the canon (although not all at the same time)

 

Another thing bothers me about the showdown with Kellogg. He has 3 synths with him, you have (vanilla) one companion. When you question him, he will not reveal where the Institute is, or Shaun's status within it. Why ? If he he kills you it makes no difference to him that you die with that knowledge. If you kill him , it makes no difference to him that you know where the Institute is and that Shaun is the director. If it was real life I would have tried to just knock Kellogg out and then torture him for the information and for revenge of course.

[TheVampireDante]

There's a chance that he doesn't know the actual location of the Institute.

 

Despite working with them for so long, I doubt the director/Division heads trusted him enough to reveal that piece of information. They'd have relayed him in, or taken him down there via some method that made it difficult to figure out the entrance point (pre-relay times if applicable).

Even if he did know at some point, they did tinker around with his head in order to fit the tech he had, so there's a good chance it was blocked/erased should he try and recall the information.

 

As for withholding the information he did know. Remember he does try and tell you do back off the entire time you close in on him. If you had taken his "advice" and left, he'd likely have just let you go since you didn't have any information to use. Telling you more than he did would limit his choices.

Having been through his memories afterwards the player can see there was a fair chance he didn't want to kill you unless he had to. Stories are too similar at points (Angered parent with spouse/child loss out for payback), maybe he was hoping you'd give up and try moving on. He only switches to attack when it's clear you won't drop the hunt.

 

That's also likely as well due to Shaun/Father/Director being involved - he may have given an order to refrain from harming you unless absolutely necessary. Which is how we all know is the eventual outcome of his meeting with the player turns out, you don't leave him much choice.

 

 

it makes no difference to him that you know where the Institute is and that Shaun is the director.

 

Again the possibility of being ordered to withhold that information might have been issued from the director - and since they are paying him and maintaining his cybernetics I doubt he'd want to disobey that one.

[Deleted40542685User]

Here's my theory,
first off the Institute was not cloning any one, they were creating Synthetic humans. The difference being, In theory cloning gives you a identical duplicate, synthetic is the creation of a new race that is made of DNA assembled in the lab. With the right knowledge DNA from a potato can be used to create that race, it is all about knowledge to properly sequence the DNA for a desirable trait.

If that is the level of knowledge that the Institute had reached, then memories could also be encoded in the brain, all memories are just the creation of synaptic links, you create those links everyday. Synth Shaun supposedly had his memories changed at the will of the Institute. After father dies Shaun the synth, makes statements that tell you that he is father. Father knew that he was going to die and the most logical solution to his death is to have his thoughts and memories transferred. Mankind redefined. Just a theory

[SirTwist]

I want to take a step back here. What I meant is that the Institute saw the cloning tech of Vault-tec, and decided to copy the technology, and also refine it in their own laboratories, not to produce the same being, with minds fracturing each generation. But, rather to use genetic material that diverse to make replacement humans. Or synthetic humans, Then they came up with Coursers. To me, Coursers are the equivalent of the T-101's from the Terminator series. The Arnold ones. Anyway, I am getting away, a bit, from my point here. The genetic material that has been collected, when Kellogg and company come to kidnap Shaun, has been fairly pure, but not enough stem cells to produce synths. And I am assuming that someone is set aside to be with the biological parent to have more kids, to keep on having kids, so the stem cells keep coming.

 

One thing I don't get, is why send Kellogg to kidnap a child, kill a parent, and leave the other alive? Why not just tag all cryo-pods, and teleport them into the Institute, Wake one person at a time, check them out, do what they need to, then send the person, returned to the pod, back to the vault? This would make more sense. Get clean, non-radiated, DNA, and other stuff, and then keep everyone there on ice. Unless there is something that will go wrong, eventually, in the vault. Before I go to far down this line, I was thinking about things. Perhaps their teleportation technology is not quite that far along?

 

I have a thought on something here. Thanks to Mighty Zog, is how did everyone get into the Vault, since the lift was faulty, and needed a pip-boy to get out? Here's one interesting idea. And supports someone coming into the vault, and releasing you. And why you have to wait for it to come down, before going up yourself. The Institute sent a person, or a Courser, with a pip-boy to get in, drop a relay grenade to teleport Kellogg and the rest of the crew in. Then they left themselves, without needing to borrow the pip-boy you eventually find on your way out of the vault. Deacon, being a sneaky bugger, had a pip-boy himself, and got in, and set a delay to wake you, then got out himself. And the put away the pip-boy, so as not to have it when you do see him again. I have a speculation on Deacon myself. A theory, if you will. I believe he might be from another Vault, but not the lone wanderer. May have had the lone wanderer's pip-boy. And came to the Commonwealth to throw a monkey wrench into the shenanigans of the Institute. And to do that, help to start the Railroad. anyway, these are just a few, brief, thoughts I have on him. I may do some more research into him, using what I can find, as well as watching again the videos on him. And start a new topic just on him. Perhaps flesh out some of the theories of the videos I find on him, and the Railroad.