You know the moment I found out Father was Saun the first thought that popped into my head was "why the fuck have your synth's been trying to kill me? Why haven't you helped me?"

I always thought Liberty Prime was Shaun.

Plot twist: Dogmeat is Shaun

I was confused due to the dialog in Kellogg's memories, if you click on the pods in his memory, he talks about "the old man" keeping you frozen instead of killing you, then in the next memory, he said that sitting in diamond city as bait was the "old man's" idea, meaning these old men are probably the same person and the fact that Kellogg did not age, even a little, proves that he is not Shaun and Father is just playing you. I think you were right, Shaun died during the harvesting of his DNA.

I think I know what the institute's motto is. "It's just a social experiment."

i wasn't buying it. the moment he tried to bullshit me i yelled "I have no son!" at the screen and proceeded to paint the walls of the room we where in with his blood.

Na... The Mysterious Stranger is a time traveling Shaun...

Also, after killing Kellog, you just eliminated his most useful asset. This also means you would be an even BETTER asset than Kellogg ever was.

I was a new dad when I first played this. It hit me right in the feels

I think that sinth kid shawn was created as a "Bait". To play the part of shawn and see how protagonist will behave. That the extreme emotion test. See how a pre-war human will act if fueled by hope.

I always thought Father Shaun made synth child Shaun as a way for you to gain all the time you lost back. give you the chance to be the parent you never got to be. that's why he was in a hurry, he wanted child synth Shaun to be ready before he died of cancer, and make sure that he would emotionally react properly to having you as a parent. He created him so that you could get a second chance at raising him. It doesn't sound too far fetched considering the world they live in.

Except Shaun's appearance is altered by the players... So he is at least related to you

I think father is Shaun but years being at the institute has indoctrinated him into thinking in such a cold calculating manner. This is to me why he doesn't help the sole survivor in the least in the beginning and middle of the game because he see's his own father/mother as a variable in an experiment than his actual father/mother because he doesn't feel any attachment to his parents. Furthermore the "experiment" if you will was also his own little test to see if he was worthy to lead the institute after his passing. But of course all we can do is specualate.

What if I made both parents black? Would Father also be black? If not, then Father isn't Shaun. He'd be an imposter!

I think that Father made up the whole story of him being Shaun because he was scared of the sole survivor. He also knew the sole survivor was going destroy the institute…unless he was made the head and joined them. And I think that the child synth project was about turning an already human (child Shaun) into a weird synth hybrid. Just my theory after playing for the first time.

I love how you never run out of ammo

Before father die, he said slowly to the sole survivor.....with his last breath.. .. .. .. "its just a prank bruh"

"Through science, we are family. The Synths, me and you". - Father. So if the Sole Survivor engages in sexual or romantic interactions with a Synth, does that make it inbreeding? Curie just became a lot creepier.

Something that keeps me sceptical is that in the memory missiln after you kill kellog, kellog refers to an old man as soon as he works with the institute. He does this before and after the institute kidnaps shaun.

During Kellogg’s memory he said the old man gave him ordered to kill the other vault dwellers. How could old Shaun give Kellogg orders to kidnap young Shaun. Shaun is the little kid not the old man

"The Old Man" is consistently used as a reference to Father. Kellogg's memories tell us that "The Old Man" gave the order to kidnap Sean and turn off the life support for all the other vault residents. this means that Father can't be Sean as Sean was still a baby, and frozen in a vault, when the Old Man gave the orders for Kellogg to abduct Sean and to kill all your nieghbours, leaving you as the "backup".

is piper really thicc?

I replayed the game and when exploring Kellogg’s brain, while staying in his house in diamond city with Shaun he says , “it’s no coincidence that the institute came to pick up the kid, then he shows up” talking something about finishing the job and killing the player

Remember the memory part where you see Shawn as a ten year old It said on the radio “oh boy piper’s really done it this time “ piper would be over hundred years old if piper was there then

need to get a dna test in the case of shaun nate you are not the father then he starts high fiving everybody and does a dance

kellog even refrences "the old man" when shooting his parent

Father is a synth because the syringer doesn't affect him, just like other synths.

The brotherhood finds out danse is a synth through institute DNA records, I've always wondered why your character and father wouldn't have run a DNA test. Where is Maury when you need him

"Kellogg doesn't seem to be aware that Father was actually Shaun" proceeds to show a clip where Kellogg eludes that Shaun is an old man.

What if the real shaun is the super mutant that can be your companion and he was experimented upon and ended up being a super mutant but he is still looking for that human milk ( the last memory he had of his moms titty ).... Think about it...

the baby they took it for research how to make mini shaun launchers

Based off of what I've seen in my playthroughs, Father can't possibly be Shaun. The main thing that I think proves this is when you are going through Kellogg's memories, and get to the scene where Kellogg is in his Diamond City house with 10 year old Shaun, Diamond City Radio is on. The radio is hosted by Travis, who sounds exactly the same as when the sole survivor leaves the vault. Now, for Travis to have been in his 20s when Shaun was 10 and still in his 20s when Shaun is in his 60s is kind of impossible. On top of that, he mentions Piper and her newspaper in the memory. This applies that Piper was at least in her late teens, likely early to mid 20s while Kellogg was still with 10 year old Shaun. When the Sole survivor meets Piper, she is maybe late 20s at the oldest, which would be impossible if Shaun is now 50 years older than he was back then. I have yet to see anyone else mention this, and I know a 3 year old video isn't the best place to bring attention to it, but I think it needs to be put out there.

You forget to mention that when you review Kellogg's memory when he is with the child in his house. Which is clearly the real child Shawn he talks about "the old man". I think it's entirely possible that the leader of the Institute is not Shaun and that he tricked the lone Wanderer into thinking he was

Shauuuuuuuuunnnnnnnnn! Best heavy rain line

Even now, every time I see Father I want to go full John Wick mode against the Institute again. Killing the spouse, stealing the baby is for me a declaration of war.

The biggest mistake in the Institute option is they are still viewed as the enemy, and the Sole Survivor doesn't dispute it saying he's in charge and they won't be kidnapping people anymore.

Kellogg also refers to Father as "the old man" but in has memories he recalls "the old man" telling him to kill the parent holding Shawn in 111.

15:13 what you came for... ur welcome.

More proof: if Shaun lived through the Kellog Kidnapping, he would be deaf.

Love the comments!!! On a serious note, when you're in Kellogg's memory he talks about "old man". He brings the kidnapping up BEFORE the kidnapping itself, and says it was a mistake for him to let you live. I feel like Father created a synth, fusing Shawn's body and his own mind. Though, just like Nick (and how Kellogg still lives within his memory after the fusion), Shawn was fused with the "old man". So in actuality, no matter how hard he tries to control this "infused mind" he cant confirm he is actually the true Shawn. Father wants you to join the institute but Shawn wants to be with you. Both minds combined must be the reasoning behind giving you a synth version of your son and allowing you to take full control. So in a way he is not your son but deep within he is. He is physically your son but spiritually (or mentally) he is the "old man". Though like Kellogg, Shawn is Bruce Banner/Hulking his attempt to show you the truth. Combine this with the video we all just watched and form your own opinion. My final inquiry is yes. Father is in some ways the actual Shawn. He is just not fully Shawn and shares a memory with the original synth creator.

Here is some evidence. When you acces Kellogg’s memories he says: “I don’t know why we didn’t refreeze all of them. I guess the old man didn’t want many loose ends.” You probably think that the Institute was run by an old man before Shaun. But Kellog refers to father as “the old man”. Also, in the Institute we find the holotape “director’s recording #108” here a female voice says that she’s not happy that a Synth malfunctioned and killed diamond city residents (the broken mask incident). This female voice says she’s the director of the Institute. In Pipers “the synthetic truth” we learn the broken mask incident was 60 year ago. That same year Shaun was taken from the Vault and in the memory of taking Shaun Kellog refers to the director as “the old man”. Weird stuff right

In Kellog's memories, when he kidnaps Shaun he mentions the "Old Man" and later mentions the "Old Man" when the Courser collects 'Shaun'

I know this is old but when you go into the memories of Kellogg during the part where he is in the cryo lab in the vault, if you click on primary patient which hold either Nora or Nate with Shawn, Kellogg mentions “the old man” and this made me think, isn’t the “old man” Shawn? Or was there another institute leader with the same nickname before Shawn? I hope someone reads this so they can try and explain it. I’m really curious.

I knew he wasn’t Shaun because of Kellogg saying he did what he did what the OLD MAN told him to do

I had a character with modded eyes. when I found Father he had the same modded eyes. I'm sure its him.

Assuming that Bethesda did not lie about Father IS your son Why side with the Institute?? Just to see your dying son?? You destroy the Brotherhood (Which Morally grey I know but still trying to maintain order), you destroy the railway that have a good intention just to see your dying son?? Come on man, not worth it.... Might aswell just kill the broken evil bastard, and make another one with Piper

As I read through comments here, it's quite clear to me, that Kellogg can not mean the same old man in all of his memories. When he enters the vault to get baby Shaun, he does on the orders of the old man, right? Right. Then some 50 or 60 years later in Diamond City with Synth Shaun he again mentions the old man. That same old man from when Kellogg kidnapped baby Shaun half a century ago? Kellog is enhanced by Institute technology, but I doubt any Institute personel, including directors, were. And Father wasn't a Synth either, as he was dying from cancer. So he defiitely couldn't be the person ordering Kellog to kidnap baby Shaun as that person was already known as old man. Which means whoever Kellogg refers to in the kidnapping scene, isn't Father/director Shaun. Thus Father may be Shaun in fact. The concept of time flowing seems to be missed with some people. Only Kellogg has those enhancements, so whatever person he was working for half a century ago, can't be the same person leading the Institute now. No one can be old for that long. Father is around 60 or so. At the time baby Shaun was kidnapped, he would be ... under a year old? Hardly qualifying for an old man back then, even hardly qualified for the director at that time. Only really qualified to be the kidnapped child. Unless some serious time travel involved, so he send himself to the past to order Kellogg to kidnap baby Shaun. But I don't think the Institute has that kind of technology, they focus more on teleportation, than time travel.

Kellogg says the words “the old man” during kidnapping of Shaun. Old man is another term for the term Father. The fishy part is, if there was another tyrannical director in the institute when Shaun was kidnapped, why do we not hear any word about him at all around the institute or when Shaun is telling the story in detail? So maybe Father abducted Shaun just because he was one of the healthy babies for stem cell medication to cure his aggressive cancer? Then Shaun died in the process? Then Father put in motion a story that he already had watching with his crows waiting for the Sole Survivor to kick Institute’s door?

We need to get Nate on Maury, to get a DNA test.

Honestly I think people are blowing it way out of proportion about the synth kid version of Shaun. Obviously Shaun knew he wa going to die soon and must have known you were going to come out of the vault soon but by the time you reunite with Shaun he will already be dying. So Shaun made a child version of himself to comfort and relieve the sole survivor of the time he never had with Shaun.

how did kellogg not age.... he was at the vault when baby shaun was taken... then he looks the same when lone survivor goes after him?

I always find the entire "is he Shaun" question thing really weird because the game doesn't really do anything to make you question it. I mean it'd be one thing if we found a terminal entry that said something like "the old man has a plan that's crazy and I'm not sure if he can convince them of what he wants to convince them of", but we don't even get anything like that. In terms of narrative, I believe in this instance it's safe to assume Father is who he says he is, simply because the game doesn't really try to give us any reason to doubt him.

If both you and Kellogg were "puppets", could Father have pulled Kellogg and the Courser's strings in a manner that hindered their ability to fight? After all, everyone expressed disbelief when you take down a Courser capable of clearing a whole building of gunners, and those who knew what Kellogg was capable of are similarly surprised.

6:17 - Wanderer: "You ain't my son, my son's Black!" - Father: "uhhhh.... I'm Trans-race.' - Wanderer: "Oh...uhh.. sure."

From my first playthrough I kept wondering, why did Father never offer to prove he's Shaun using DNA testing?

I personally think it’s messed up taking synth Shaun as a son, he’ll never age and it’s literally replacing what would’ve been your actual son with a fake, he’s still sentient but it’s messed up. This is why institute scientists were against it.

I believe dogmeat to be a synth placed there to help you. He's the only one allowed with you in the institute. Also the only German shepherd in the entire game

What if the real Shaun died and they need the back up , but father knew he would not help if they killed his son. So father says he's Shaun so you can help him

ik this is old but i just did another playthrough and kellog mentions "I don't know why we didn't just refreeze them (other vault dwellers), i guess the old man (maybe shaun?) didn't want too many loose ends" this made me jump up because shaun is in the cryo pod at this point which means he isn't the son unless he killed the vault dwellers while we ourselves were in cryo and went back even after they kidnapped him also kellog isn't aged at all from shaun being a baby to the old man part, which means a lot of time didn't pass between the kidnapping, i personally think the synth shaun is actually our son but "father" implanted a cybernetic in him (evidence is kellog's implants) which could easily have a deactivation code and since the father's face changes with yours i believe hes a synth himself and just like deacon got facial reconstruction to convince us to help the institute. Edit : forgot to mention he refers to shaun as the kid and not "the old man" aswell

The most compelling evidence is that EVERYONE remembers Shaun and Kellogg living in Diamond city. As Father said, kid synth Shaun was a work in progress, he wouldn’t let him go with Kellogg AND he’d been with him for a while according to Kellogg. Also Travis miles playing over the radio.

6:16 i think his wife got a little frisky with the neighbor . Shawn wasn't his in the first place

yes, i made a character with massive cheekbones and no chin. Shaun had the same features

This guy is like: remember no brotherhood knights.

How I see it is that Sean grew up in the Institute, with a bunch of uncaring and cold scientists that did not give him the paternal love he would have needed to grow into a fully functioning adult. Because of this, he probably became a sociopath, continuing immoral experiments because why not? Doesn't matter to him. The Institute in underground and separate from the Commonwealth, and so the trials and tribulations of the surface dwellers may not even be anything other than variables to factor into an experiment. Because Sean grew into being a sociopath, when becoming Director, he learned of everything about his past, and it planted the seed of curiosity in his mind. When faced with his own mortality, he began to have an internal dilemma, and was faced with new emotions he hadn't experienced before, but because he grew up without loving parents, he didn't know how to process his emotions. So creating a child version of himself and releasing you from the cryostasis and setting up this whole chicken run was his messed up way of trying to reconnect with his long-lost parent in the only way he could rationalize it to himself, a scientific experiment.

Both Shaun and synth Shaun disliked the video.

(taps on to the video) Yes. Yes he is. (leaves)

Here's the thing with Child Synth Shaun, I do actually feel the Shaun we were after thru the story was the synth Shaun, you see. In the storyline we're told that only coursers and synths have the technology to teleport out of the institute at will, as they have microchips which allow them to attach to the frequency of the institute, this is how they get out/in, obviously. During Kellogg's memory flashback, the final memory is Kellogg and Shaun within the household, as the courser shows up it proceeds to say Shaun's name and exact location almost as a coordinate, from there the Courser, AND Shaun teleport into the institute, now. Later down the line if you side with the institute you gain a microchip that let's you teleport in and out of the institute at will, here's the thing, this chip is implanted into your Pip-boy, not you, as they only do this with synths. That's just my take on this situation.

Dr Li was lied to by Father about Virgil and the FEV lab. Virgil left, and Dr Madison Li will too, when given the evidence how corrupt The Institute is. I think it feels like the faction was redesigned and they patched up 3 story arcs hastily without thinking if it would be consistent.

No I figured out that he isn't. When you access Kellog's memories, in the memory inside the vault, when you press on a cryopod, he says " I don't know why we didn't refreeze all of them. I guess the old man did not want many loose ends. Thus suggesting that the Institute's director at the time, 60 years prior was an old male, like the father. Furthermore, in Kellog's next and final memory he even refers to the father as the old man. Finally inside the Institute, you can find a holotape named director's recording #108. There a female voice explains how irritated she was about the fact that a synth went in diamond city and killed many people due to a malfunction. That voice presents itself as the institute's director. However by reading Piper's "The synthetic truth" article that this event happened nearly 60 years ago, at the time Shaun is supposed to be abducted. Thus the Institute's director at that time was a woman, which comes in contrast with Kellog's memories. This would suggest that Shaun was abducted more recent, and that the Institute killed him or raised him, and now he is a scientist there unaware of his situation. Combining that with other plot holes that are created, that are mentioned in the video, and with the fact that your first encounter with the Institute seems staged, you can conclude that the father is just the director, who wanted to conduct an expirement.

Something interesting that proves the synth that thinks its Shaun is a synth, or just not human, is that with the power armor modification that highlights living targets, Shaun doesn't get highlighted like literally every other NPC in the game

It should be mentioned that in the memory sequence you can hear the radio host complaining about Piper (the memory of Kellog's house), how is piper at the oldest like 30 something after you wake up, when Shaun ends up being 70 something. Either Piper can control the flow of time and make herself younger, Father is full of shit, or Bethasda is full of shit (bad writing/not controlling what's on the radio, which doesn't make sense to me because a very fitting song, "it's all over" plays when that memory begins to end which seemed to fit the tone, and thus seemed the radio was paid attention to)

I have a theory. When you go in Kellogg’s memories, you see him with Shawn. Here is the thing, if the kid Shawn was a synth, he would have been able to teleport on his own. Just a theory.

I think there's a 10 Year Old Synth Shaun and a real 10 Year Old Shaun. When you access Kellog's Memories, he says something about 'The Old Man hates loose ends'. That could easily be Father. The Synth Shaun was there to trick you into believing that Father is Shaun while the Real Shaun was released when you try to blow up the Institute maybe as a gesture of 'Okay, you won. Here's your prize.".

Apparently people didn't pay attention to the story, so let me clear some things up. 1. Father is Shaun 2. Kellogg is a cyborg 3. Father is over 200 years old 4. Kellogg is about 100 years old 5. The Sole Survivor is over 200 years old 6.Kellogg became employed by the institute and took Shaun from vault 111. This is when your spouse dies. 8. Shaun was taken 60 years before you wake up the second time to go find him. 9. Over 60 years and Shaun is now Father and now runs the institute. He releases you from cryo-sleep. 10. Father has a child synth made to look like him so you would have hope of finding the real Shaun. (Father) 11. You fall for it and think Shaun is 10. 12. Kellogg has the boy in Diamond City a little bit before you get there. X6-88 comes to take synth Shaun and gives Kellogg orders to hunt down the escaped head of bioscience Dr. Virgil. 13. You track Kellogg to Fort Hagen where he was getting ready to go into the glowing sea to find Virgil. 14. You kill Kellogg and realize he was a cyborg and thats how he looks the same as when he kidnapped Shaun 60 years prior. 15. This makes Kellogg about as old or older than Nick Valentine. The exact time of Nick's creation are unknown, but specualted to be about 30 - 40 years ago, when gen 2 / gen 3 synths were being prototyped. 16. Go play the damn game so I don't have to explain this. (Age When They Die) Father: ~ 210 Kellogg: ~100 Sole Survivor (Leaving Vault 111) ~ 240

If not, where is he? Could he be the lone drifter in Nevada? Perhaps he is the Mysterious Stranger?

But what’s interesting is that whenever Kellogg talks about Father, he mentions the old man, and then when he mention about shaun, he just says he’s a little older, plus kellogg mentions word about the old man when he first kidnaps baby shaun thus proving Father is not shaun

Confirmed, Puma is black and is named DeShawn

Then how old is Kellogg? He kidnaped Shuan since he was a baby. And then Shuan become an old man but kellog still look the same.

Considering that Shaun's facial model is always an amalgamation of Nora and Nate's at the beginning of the game, I think the answer is a resounding *_Definitely yes._* If you make Nora and Nate both have a big red nose and have no hair, Shaun will have a big red nose and no hair.

"I Guess the old man didnt want so many loose ends"~~

I think Father wanted the Shawn Synth experiement to be done quickly because he knew his survivor parent would be there to see him. So when he dies of the cancer after telling his parent he was Shawn they would have a piece of him left. I get it omg

i need someone to please help me understand this when Kellogg takes baby shaun Kellogg is about lets say 40 but when father says its been 60 years how is Kellogg that old he cant be

To me, all of this seems to point to the Soul Survivor being a synth more than it does to Father not being Shaun. It is very clear that Father treats the whole releasing you thing like an experiment. That would make sense if you are a synth who could be replaced if something happened to you. And if you are a synth of Father's real parent, programmed with all of their memories, then I would understand why he would be so warm towards them when meeting. He's getting the chance to find out what would have happened had you not died. He gets to know that you would have gone to incredible lengths to save him. Since he is dying, of course he would want to know those things before he goes and luckily (or unluckily) for him, he is in a position to actually find out. He leaves Kellogg and synth Shaun for you to have a trail to follow, but if he were to just have the Institute fetch you, there would be no point. He wanted to know exactly how far you would go to get to him. (He also probably wanted you to get rid of Kellogg tbh). I feel that SoSu being a synth answers most questions in regards to Father and what he does to you. The only thing I'm still left wondering is why Father would leave the Institute in the hands of a synth.

Shaun´s actions towards you might be explained with the idea that you are not human. You might just be Shaun´s experiment. His attempt to give his family a second chance. Most likely you are redefined courser. After all you are unlocking new skills and getting stronger as time goes on. Way more than what would be humanly possible. Letting you to "escape" the vault was an experiment on how strong your "love" would be. And how would a synth behave if left with his/hers own devices.

Someone should just make a mod where synth Shaun is the real Shaun and father is just tje leader of an evil faction that needs to be taken down. Also the game needs an end boss not just kill some mobs and game over.

I think the synth shaun is built to give Nate/ Nora some closure and give his dad the wish to raise a child and father can see how great of a father he really is

In my first playthrough I thought Shaun had actually been killed and harvested by the Institute and Father was simply lying to get you to do his dirty work

I always imagined it like Stephen/Thomas in the Maze Runner where they took constant blood samples and tested his knowledge while teaching him new things at an accelerated rate.

What confuses me is the ages/time. Kellogg takes baby!Shaun and then what? 50 years later they give him a synth!Shaun who is 10 years old? Kellogg isn't like why isn't this kid 50? And does Kellogg have implants that keep him from aging because he was probably middle age when he took baby!Shaun but he looks no different when you confront him later. Did Father rapidly age from baby to senior citizen in a decade? Did I miss something in game or is that just really bad writing/math? We know there is a Preston Garvey impersonator so why not a Shaun one in Father? The real Shaun probably died in the procedure to get his DNA. If that is even true either.

Regardless of what happened to Baby Shaun, the story is brutal and horrible, just like war. This is the story of a baby cryogenized, then taken away to be raised by strangers who did not treat him well in an post apocalyptic world full of horrors, desolation, and well... turned into THE wasteland. His fate was perhaps the fate of all babies who were alive at the time the bombs fell in 2077, at least the fate of those who survived as orphans to fend for themselves in such a world. The story has all the brutality of real war. It's really sad and disheartening, as happens to any war child in real life.

When we reach the memory of the Institute abducting Shaun, Kellogg mentions how he "wondered why they didn't just refreeze the rest of them". Then he brings up how the "old man" didn't want any loose ends. In the very next memory, we see Kellogg and Shaun living in Diamond City. X6 comes and takes Shaun, and Kellogg wonders if the "old man" had outsmarted him- if he was just another loose end that had to be tied up. Are all Institute Directors Old and males? Again Bethesda left very little to work with... But here's the big kicker that blows the water out of Father's alibi. DIAMOND CITY RADIO. We hear coming from the radio in Kellogg's house the voice of the one and only, Travis "Lonely" Miles. How can that be if Shaun was only 10, and Father is 60? Travis also mentions Piper's paper, Publick Occurence, AND Piper's ongoing feud with Mayor Mcdonagh. So unless Travis and Piper are somehow over 60 years old, Kellogg's time with Shaun in Diamond City was very recent. Dr. Amari even said herself that this was a "recent memory" of Kellogg's. Now some say it is synth version of Shaun, but this is not enough proof.

I think the majority of these points have to do with messy writing on Bethesda's part tbh. It's fun to explore the space and try to put together what actually happened, but I don't exactly think they were playing 5d chess. I wouldn't at all be surprised if them adding in the whole "is the player a synth?" thing in Far Harbor was a result of them seeing fan theories about it and realizing it would fill in several plot holes

Really? Video attempts to answer: 'Is Father Really Your Son Shaun?' Conclusion: 'Dunno, might be, might not be' But this video sparked my interest to find it out for myself, so I did and found the following. If you find the records of Dr. Madison Li you hear her say the following in one note: "I think he's actually lost his mind. I can't believe he really expects me to do this... I have always been on board with the Gen 3 program. It makes sense. But this... nothing good can come from this. How am I supposed to explain to my staff that Shaun wants a child synth, for no immediately apparent valid line of research? And to base the physical features off records of his own childhood? It defies all logic. No, I can't do this. I won't." And in another note: "This is day... eight of trial six. The last week has been very productive, but exhausting. I think we'll need a break after this. Binet has done some really marvelous work with the personality mesh. It's... well, it's almost too good. The responses map almost identically to expectations... Some of the most life-like I've seen. Of course... It's not really Shaun. None of his memories are in there. That, even now, would be a step too far. It's starting to have an effect on the team, I think. I know I've been caught up in the moment once or twice... Just a second or two... forgetting that he's not a real boy. Still, I think we'll need to consider restricting him to the lab only for the moment. I'm well aware that others are... put off by his presence. If I were slightly more arrogant, I might consider that a sign of success..." This all points to Father really being Shaun, your kidnapped son and not a clone or someone completely different. Since none of the other people you get info from actually truly knows, except for Father/Shaun himself but his trustworthyness is highly questionable, this is the best evidence we can find. Conclusion: Father really is Shaun. Case closed.

The other thing that says Father is Shaun is the way that his model changes with how you create yourself and your spouse at the beginning, similar to how your father James changes skin tone and eye colour depending on how you make yourself in fallout 3.

I think you missed a major piece in all this, when going through kelloggs memories kellogg himself mentions the old man, father, during the mission of taking baby shaun. He mentioned him in a way that suggested that the old man gave the order to retrieve baby shaun, he also wondered if the old man used the sole survivor to kill kellogg and tie up loose ends and if he outsmarted him in the end. All of that suggests that the old man is the leader of the institute and someone other than shaun. Kellogg would know by his own age who the real shaun is and wether the shaun he had with him in diamond city was the real kid or not just by age alone. The old man was the old man, the kid shaun was a synth and the institute kills the original subject when making a synth copy. Shaun is dead, father is the enemy, the synth shaun is the copy of your son, and you got out of the vault and no one expected this. The vault dweller was a tidal wave no one could stop or prepare for and so father had to come up with a way to stop you, or use you, so he gave you what you wanted to make you behave and tried to use you. Either way, i think Kellogg is the key to knowing wether father is shaun or not and based off of what you see in kelloggs memories id say that father isnt shaun, or at least the developers left some serious discrepancies in the game to refute their own narrative.

Here's my theory. Shaun did assure your survival, at least to a certain degree. He's a genius, and was raised around brilliant minds and without emotional interference. I think that he placed synths in the other major factions and manipulated them into leading you to the institute. Each major faction has a synth that you will have at least some relationship with helping you to reach your goal. With the Minutemen, that is Sturges. With the railroad, take your pick. With the brotherhood, Paladin Danse. These three are probably bugged (the only one I doubt this with is Sturges since the Minutemen aren't significant enough to warrant patrol), and are used to guide you to meet Father. I also have a theory that this is the role that Dogmeat plays as well, since they go out of their way to prove that they also know how to make animal synths.

but shauns appearance changes with the players

I hate theories like these. At start they tell you the opposite of what you thought, but later they just show that what you thought was actually right. Therefor making the whole video pointless.

We have to remember that fallout has the ability to clone people and completely reconstruct a real person. From my theory. Shaun was needed for his DNA. He didn't have any radiation in his DNA. I would say that Shaun was either killed during lab research or thrown away after the institute was done with him. Other theory is that shaun was sold off to another faction that needed a specimen without radiation. The only one that comes to mind is the enclave, however there is no evidence that the institute works with the enclave. Just the history of the institute being prewar and the government would've known about them. I think the truth is that the sole survivor was just kept if the institute needed another specimen for their experiments. However they didn't. So the next experiment was to see how a vault deller would do in the post apocalypse world starting with nothing. I would say everything was going to plan, but you entering the institute was not part of the plan. They didn't try to bring you in. You have to break into the place. The shaun synth was probably created for two things. 1: to start making synth kids. This could be so people stop seeing them just popping up as adults. It also helps them stay hidden in the world because no one knew they made kids and people are usually less suspicious of children. 2: was a failsafe if the sole survivor has filled their experiment. So they would just leave him in a spot with a memory flash. That would've stopped the progress of the sole survivor from getting into the institute. However I don't think the synth shaun was fully done yet, which explains the giant rush that father had with him. As for father. I think he just reconstructed himself to look like shaun. I don't really think he is the sole survivor's kid. He definitely shows no real care about you on leaving. He already knows that the commonwealth hates snyths and that you would likely end up not liking them either. So if the sole survivor got into the institute, knowing everything about synths from the general public so far and from their experiences, they wouldn't take anyone there as a good person. So father being shaun was something that you would likely forgive. Thus the chance he gives you when you enter the institute. How would the institute know how to reconstruct father to look like shaun grown up? Well they had baby shaun to begin with and they also had many cameras on you while you were roming the waste. I would also say they reentered the vault and got photos of you frozen.

If the Sole Survivor is a synth, it all makes sense with Father being your son.