Fallout 4: The Ugly - The Institute

When first entering the Institute, you are given a promise by Father that 'all your questions will be answered'.  That is a lie.  You don't even get to ask them.  I had a lot of questions about the place and its people, and trying to find anyone with any expansive dialogue was a dead loss.  None of my questions about how the organization is run, how it manufactures materials nor even the basics of why there are so few people there could be answered because the questions could not be asked.  I wanted to reserve judgement on it until I could begin to understand some of the nuts and bolts of the organization, its structure, its accountability system, and how it determines just what projects are and are not important plus what the prioritization system were.

Without those answers even the most simple and most basic question of asking: what does it mean to be in an Acting position comes forward.  In our common understanding, when an individual is an Acting Director or Acting CEO or other, similar position, it means that they are temporarily in that position until a final individual is found to put into that position on a full time, full authority for that job basis.  With the Head of the Synth Retention Bureau, Zimmer who appeared in FO3, out going after 'high profile cases' the PC gets to meet Justin Ayo who is the Acting Head of SRB.  Thus the Institute adheres to this concept of an individual acting in a position who is actually the #2 person or the designated temporary stand-in for the actual person who has full authority.  Justin Ayo can, therefore, be over-ruled if he is seen as stepping beyond the limited authority granted to him as the Acting Head of the SRB, and his intrusive manner and paranoid attitude towards the scientists in the Institute has many complaints filtering upwards.

If this is the case then when meeting Shaun who is the acting Director of the Institute, then the natural question, indeed the very first one that came to my mind is: where is the actual Director?  I don't want to talk with a stand-in, but the actual person who has real authority inside the place.  The further designation of 'Father' is not an actual position nor title, though it is enough weight to sway the subordinate Heads of departments whenever Shaun makes a decision.  It is a truly minor point, of course, since he is considered the actual Director for all intents and purposes, but it is Shaun, himself, who gives himself the 'acting' designation and he should know what that means inside an organization.  If it meant he has the full power of the Directorship, then he could simply dispense with it and say he is the Director, no 'acting' is needed.  The suspicion is that what the PC sees and encounters is rigged and a set-up to protect the Institute, with at least two figures of power (Head of SRB and the Director) actually off-stage in case Father's harebrained scheme goes awry.

That is just a first glance problem with 'answer your questions', and yet the questions continue far farther and deeper than that.  In journeys through the Commonwealth, the PC can go through University Point and find what the Institute was looking for: the Laser Rifle with the 'Endless' Legendary effect.  Kellogg led that attack after first just giving a simple demand to hand it over, but since no one had actually figured out what it was that the pre-war researchers were actually looking for or where to find it, the Institute got no answer.  For that, they were slaughtered and synths sent in to comb the place for the project, which they didn't find.  On suspicion of having important pre-war research, an entire trading town was slaughtered: every man, woman, child and food animal was killed ruthlessly.  As this was under Father's Directorship, he had to give the OK for it.  I wanted to ask him why this mission was authorized and finally give some closure to the entire affair as I felt the technology was underwhelming.  This is an event that many NPCs will mention in passing, and has reverberations across the Commonwealth as University Point was an important trading center, so its loss put a financial hit on many across the region.  Yet no answers can be found within the Institute, and the current leadership hasn't gone through any turnover, so getting an answer from someone should be possible.

At this point the game mechanics of being an Action game with RPG elements goes against role-playing as the player is expected to just accept that they will never get to ask substantial questions and get actual answers.  To create a deep background to The Institute would require much more voiced dialogue from both the PC and NPC's inside the place, and give the player a certain amount of agency in making decisions about The Institute.  It is to be remembered that this is the very first time that the actual Institute has been open to play in the Fallout franchise, and understanding its background, position, operations, methodologies and how it works are vital in determining just what sort of future it should have.

The Institute wants to be low profile, and yet actively antagonizes, indeed wantonly murders, kidnaps and replaces individuals on a whim.  The Mayor of Diamond City is one thing, but what about poor old Art?  It is a random encounter but finding Art vs. Art, two identical men going after each other because of a botched synth replacement, is telling.  First off, Art (the original person) doesn't hold any position of power, influence, and is, for all intents and purposes, just another wastelander of no importance.  If he was important, then this wouldn't be a random encounter, now, would it?  Yet this no account wastelander is on the line to be snatched and replaced.  So why not do that with someone at University Point and get a first-hand look at things and not expend as much time and effort combing through the ruins in a vain attempt to find something that was only hinted at being there?  No need for Kellogg to show up, no threats, just a replacement of one of the individuals without a family to then keep an eye on things and ask some low key questions.  Through the use of the Molecular Relay, it should be possible to do this and gain INTEL without a huge expenditure of resources.

This only makes sense if The Institute wants to keep an element of fear and terror inside the Commonwealth, and breed paranoia.  An organization that actually wants to keep a low profile does not operate like this in the open leaving traces and evidence behind that is easy for all to see.  For all of the bluster and verbiage about being so advanced and the wasteland having nothing to offer The Institute, and wanting to have no hand in the affairs of the surface world, the organization sure has a funny way of going about it by doing just the opposite.

As presented The Institute has little idea of how to actually manage projects which, given the nature of research and technology, should be something they would be good at.  An example of this is the need to get a new reactor going to power The Institute, as given use the old systems already present or made just after the Great War and siphoning off of topside systems is causing major problems.  It would have been nice if every time the PC uses the teleportation system that, when they arrive, there is a major brownout and perhaps some people being a bit PO'd at this constant abuse of a privilege. Verbal indications just don't cut it when you have such a new and fancy setting, and would put a real sense of understanding into play.  Still the plan to actually build and start the new reactor hinges on a vital piece of technology that no one has seen and only has a few vague descriptions to go by, but is powering a huge system in the Mass Fusion building (currently occupied by Gunners).  The BIG MISSION for The Institute and Brotherhood (who need the same piece to get Liberty Prime up and running if you go their way) is that McGuffin in Mass Fusion.

This begs the question:  how can you even start a project like this if you don't know the exacting specifications of the piece that is vital to it?  The answer is: you can't.  In fact this isn't the last piece you want to procure, but the VERY FIRST PIECE as it is vital to the design of the rest of the system.  Even if lesser pieces of the same dimension had been used previously, this one has new interior power design parameters which indicate it can do much, much more than prior versions and would then allow for a much more capable system to be designed.  If you knew those specifications, that is, and had the piece in hand to see if it actually worked as the single piece is just a WORKING PROTOTYPE.  Yeah, all the bugs weren't ironed out from it, but being functional meant it would be sent to the US military pre-war, which would mean DC.  For a brand new, long term power system, wouldn't it be nice to know if the critical component that will let it power up and function actually had long-term components in it and had actually operated within design parameters?  Wouldn't it be nice to KNOW those design parameters?  And if you knew all that, then why not just make one?

This is a Project Management failure of such large proportions that I found it impossible to give any credence to the idea that The Institute was competent at manufacturing and designing technology in its current state as shown.  For a project you need to gather specifications and materials before you actually start on it, and critical fail components need to be secured first on the list, not last.  The Institute has had years, if not a decade or more, to actually accomplish this and yet, wait around until they build everything then HOPE to get the necessary part to make the new reactor work.  As I've said in other settings: Hope is many things, but it is not a strategy.

So far an overall view of The Institute comes off as bi-polar, dysfunctional, and incompetent.

To me, as an individual player, the attraction of helping this group got marginalized very quickly, and yet all of this gets summed up in what is driving the organization forward.  The simple motto of "Mankind, Redefined" is one that has been heard a few times, and usually has the slaughter of millions of innocent people at its feet.  Be it Stalin, Mao, or Hitler, when this concept gets a head of steam going the results of Collectivization, A Great Leap Forward, or Purifying the Race are the types of results at the end of it.  "Mankind, Redefined" is just a motto that drives the Gen 3 Synth program, but no one wants to actually put hard and fast milestones to what it means.  To actually reach an objective, which is what the Gen 3 program is all about, there must be certain and attainable goals and end state that can actually be stated and defined.  If you can't define the end state, then how can 'Redefine' ever be achieved or even started?  That motto sounds great as a sales pitch by a Department Head at a meeting, but if it isn't backed up by a concrete proposal leading to a verifiable and achievable ending, then it won't go anywhere.

Thus the Gen 3 Synth program has a Project Management failure at the start, just like the new reactor program.  At least in the case of the reactor, the piece is known to exist.  For Gen 3 Synths, without such a definition the entire concept will turn into a programmatic Death March of constantly shifting goal posts, wasted months or years of effort, then working towards the new goal and facing the exact, same redefinition.  There are indications this may have started as a Spiral Design project, and yet even those have verifiable end goals in mind with milestones that can be checked off along the way.

And the Gen 3 Synth program is eating up resources, using up lots of vital power and is impacting projects across The Institute, which lends political power to both Advanced Systems and SRB.  There is one researcher who WILL ask, rhetorically, just what that motto actually means, and he is Lawrence Higgs.  There is a lone dissenter to the entire Gen 3 Synth program because it doesn't have a meaningful end state that can be defined.  He is meant to come across as old fashioned, but Lawrence Higgs is the only one to posses the actual clarity of thought to put the entire program into question and he is loyal to The Institute.  The institutional clout of Advanced Systems and SRB is also felt in the leeway granted to Justin Ayo and to Madison Li.

Madison Li has problems with Father wanting a duplicate of his younger self made as a Gen 3 Synth experiment.  While on-board with the entire Program, this personal project of Father's starts with misgivings by Madison, as heard on a holotape, and a later holotape shows some appreciation of the project and some apprehension as well.  To her the Child Synth concept is troubling to her since she knows that synths do not grow old and, thus, a Child Synth will not grow up as the goal is to redefine mankind, and growing older and maturing seems to be out of the question.  Gen 3 Synths receive programming that only allows for limited learning and ability to question what they are doing, yet large leeway in that ability to question and store the answers.  In trying to constrain curiosity and self-awareness, enough of each is provided to Gen 3 Synths to allow them to break out of their programming constraints.  A child, any child, must have much greater curiosity as they do not have much in the way of experience nor a mature way to process information, and thus a Child Synth must have those traits and yet have them heavily constrained so that they never stop being a child.  This is a recipe for disaster, which is something that Madison Li has to deal with, and the lack of rationale given to creation of this Child Synth add to her suspicions about the motivations of The Institute and Father as the Child Synth project can only be a dead-end.  A dead-end likely to end in some form of psychosis of the Child Synth if allowed to continue for the long term.

The very mental stability of Father, the child of the Sole Survivor now over 60 years old, must be called into question at this point.  While pointed at as a 'Great Scientist' the PC never gets to see just what it is that is so great about Father.  He acts in a humble manner (and the great work on animation has his stance and gestures show that he is clearly not telling the truth when you first meet him), and only cites his genetic background being the one used to create the Gen 3 Synths as the major reason for his elevation to his current position.  While a leader of The Institute, he shows no real Program Management skills and allows programs with ill-defined or non-defined goals to continue, gives the OK to a project that can't even figure out how to get the most valuable component as a first task, and then over-rides the specialist knowledge of a Department Head to authorize a project that is not just counter-productive but can only lead towards failure in the Child Synth experiment.  To those inside The Institute, driven on by a motto, he is a 'success' but try to find out what he was successful at doing, and you get nothing.  No awards, no accolades, no demonstration of technology, and no evidence of actual leadership skills, either.  He over-rides Department Heads without giving reason, shuts down the FEV lab and hides what is going on, and generally gives wide latitude to a paranoid head of the SRB to act as a form of Secret Police.  On top of that he also manages to leave out that he has terminal cancer as part of his condition until the very end, and that is the reason he has acted so rashly.  Cancer is, however, curable in the Fallout timeline, and one would think that the medical capacity of The Institute would have dealt with that as part of the Gen 3 Synth program, at the very least, to stop the unconstrained growth of cell cultures taken from Shaun.

After that there is the problem with the population size of The Institute.  There are two children and one young adult within its confines and the total number of individuals is under a hundred (and that would include people out on missions and such, like Zimmer).  This is not a viable gene pool.  Even taking in a talented individual or two from the wasteland doesn't get a viable gene pool, and it is questionable if those brought in would even be allowed to have children, given the entire viewpoint on how those inside The Institute value their less polluted gene pool in comparison to the surface world.  What we see of The Institute is the last generation of humans there.  As Gen 3 Synths aren't seen as people, but as property with some cognitive ability and that Gen 3 Synths are not able to reproduce, what we are given is the End of The Institute within a few decades.

This is a problem of the entire surface world as depicted, of course, but is acute inside The Institute as means to garner individuals and more diversified genes were deliberately destroyed by The Institute itself.  This happened when the people and their genetic material in Vault 111 were killed by Kellogg and Institute staff.  As seen in Sanctuary as the bombs dropped was a diverse gene pool and age range that would be reflected inside the protected Vault, and only a very few individuals were exposed to the bomb blast that had the Vault go to lockdown.  It is to be noted that Shaun was amongst those individuals, and his genes were declared to be pure enough to pass whatever tests The Institute had.  What about all the people who made it down BEFORE the bombs fell?  And if the brief exposure at such long distance wasn't enough to damage an infant's genes, then what about the adults, including the parents of Shaun? The Sole Survivor is called 'The Backup' which means that, yes, the genes from those riding down on that fateful day would ALSO be candidate genetic stock for The Institute.  And even those in cryo failure before Kellogg arrived are in a state of suspended animation, kept at low temperature and should have much viable genetic material in them...and there is always the possibility that advanced medical techniques could revive them.

Surely those inside The Institute, particularly the BioSciences division must have run the numbers right after the survivors of CIT got things settled down beyond base survival needs and recognized the major problem of their population size and lack of genetic diversity.  To a degree this is a problem in Vault 81, as well, although they have a system of 'population control' which must also have genetic viability management as part of its design.  Even with that Vault 81 is in the same position as The Institute, although it may be better managed to allow for multiple families to have children so that there will be a future generation of Vault residents able to maintain and manage the place.  Not so with The Institute.  The grand and quite spiffy place they have made for themselves is less well managed than a Vault-Tec Vault that has adapted to stringent population controls and genetic diversity management and are slowly opening up to the idea of more trade with the outside world, possibly due to the condition of the Vault and overall lack of genetic diversity in the population base.

These are the problems with The Institute we are shown in Fallout 4.  Yet with one of the division heads and an indication that the actual Director may not be Father, there is a sneaking suspicion that this is not the totality of The Institute.  To last as long as it has requires a much larger population and more in the way of foodstuff production than can be achieved in the BioSciences labs.  As for the new Gen 3 Synth we see stroll out of the creation room, well, where does that door go to?  I mean if you do a quick check using the console, you'll see that you don't get a new synth out of the room but the same one over and over and over again.  Maybe it is a test model that is immediately broken down?  If you take the given production rate at face value, then The Institute, as shown, would be over-run with them in a few days.  It can be assumed that Gen 1 and 2 Synths are just put into a shutdown state someplace and activated as needed...though there would have to be one heck of a storage facility to account for their numbers.

A final piece in this is that The Institute is the progenitor of Super Mutants in the Commonwealth, and there are no indications of outside Super Mutants showing up there.  A top number of Super Mutants dumped in the wasteland can be figured out based on the size of the FEV lab in The Institute, a rough measure of how many abductees are processed per month, and that multiplied by ten years to get a total maximum number of Super Mutants put out by the FEV program.  In taking off attrition of Super Mutants due to Raiders, Gunners and the hazards of the wasteland, plus simple in-fighting, that total comes down with an upper limit (if being generous and underplaying the hazards) of 3,000 Super Mutants total and a lower limit possibly as low as 1,500 being the absolute total number at game start.  The Sole Survivor kills of quite a few of those, and many more are killed off due to those hazards of the wasteland deals.  Put in the places that they have taken over having Raiders and Gunners as neighbors, and that lower estimate starts to look pretty generous.  Yet there appears to be an endless supply of Super Mutants.  Of course this is a broken game mechanic that makes no sense, but if you want to make sense of it, then the only real solution is that the holder of the FEV has another facility set up somewhere.

The question that comes from this is:  Is The Institute we are shown in Fallout 4 the real thing?

Everyone acts suspicious and is tight lipped about The Institute, even if you get friendly with them.  All the interior plot lines support the glitzy showcase as being The Institute.  Yet it doesn't have the infrastructure, facilities space, production space or population size to support itself to validate this concept.  It is a showcase, a place where all the new technologies come together to show the promise The Institute has to offer, but even this showcase has problems keeping itself powered up.

If we accept the game mechanics as true, then The Institute we see is not the real deal.  In fact it would need to have a much larger facility, perhaps using multiple pre-war generators, and be pretty far from the CIT ruins.  This would make sense as the survivors of the old CIT would realize the need to gather other survivors with technical knowledge to survive longer and the immediate shelters and systems they made would only serve as a base of operations until such time as a better and safer place was found.  Perhaps an old military base or underground storage depot in the western or north western part of the map.

In my first play through I used this logic to search for The Institute as I thought there might be some clue or a DIY way to get into the place.  Roaming across the northwestern part of the terrain, I found a number of large pipelines heading underground and searched, in futility, for where they were going.  This part of the map is one of the least threatening places in all of FO4 and it appeared to have the right amount of water infrastructure heading into it to support a large organization.  An added bonus was being near Vault 111, giving them easy access to at least the remaining above-ground supplies left after Vault construction.  All it would take was an old, underground military supply depot or bunker (like we see in FONV) and The Institute would have a relatively safe, quiet, cozy home and use the CIT base for putting together the future of mankind, supported at a distance just to insulate the real Institute from harm.  Given 3 out of 4 endings to FO4 this would be a smart thing to do.

What is fascinating is the mechanics and results of quests handed out by Institute members concerning synths out in the wild.  In Synth Retention and Building a Better Crop, the Institute sends the PC on missions to Libertalia and Warwick Homestead: the first on a 'bring 'em back alive' deal for a rogue synth and the other to help iron out problems the Bio group is having in testing out a new strain of plants.  On a later restart of the game, I decided to put an idea into action to test the veracity of the two individuals (Gabriel and Mr. Warwick) being synths, as well as generally trying to fail the missions as they are amongst the very few the PC is actually allowed to fail in completing them.

First was removing the old ex-Minutemen turned Raider contingent in Libertalia before getting Synth Retention.  Why?  I wanted to see what happened the next day when I got the mission.  I fully expected the Raiders to remain dead, but that didn't happen.  Yes the game mechanics require a fully stocked and prepped set of Raiders encamped there, and that is what happened: it is pure game mechanics involving the quest and nothing else.  Yet that makes no damned sense, now, does it? Literally, overnight, all the bodies were removed and the entire place reset during the few hours I spent back at the Institute.  If anyone had to explain this as a real world phenomena, then it would involve high technology, teleportation and a group of very quick working actors put in place to make the site quest-ready.  Going down this line of reasoning then eliminates the Raider gang under Gabriel as being one that opportunistically moved in right after the prior gang was eliminated: they would require a lot of help to do that and Raiders are not known for their work ethic.  Nor are they known for hacking capability to change or delete computer entries on terminals referring to the prior gang.  This is the realm of Institute work since they fit the bill for doing all of this if they had a Raider group under the control of an operative who organized them, and the Raiders have loyalty to this individual.

That is a big 'if'' and would require putting a Gen 3 Synth in charge of Raiders.  The way the quest is supposed to go is that Gabriel is given his factory recall code (after cleaning out the rest of the Raiders below the highest point in the array of ships), and then kill off the few remaining high ranking members.  After that X6-88 transports Gabriel out of there and the PC is left to figure out just what happened.  Yet there is a very slight window of opportunity at the very start of the meeting to pull up VATS and target Gabriel.  By then I had a fully tricked out Gauss Rifle and maxed out Perk trees for Rifleman, Ninja, Mr. Sandman and a couple of criticals stored in Critical Banker.  Goodnight, Gabriel and hello to mission non-success.  The rest of the Raiders were easy to take out and I got to Gabriel's body to take a look-see.  Gen 3 Synths, on death, have a Synth Component available in their lootable inventory.  Danse has one, Magnolia has one and the Mayor of Diamond City has one.  All Gen 3 Synths found dead to other causes have one.  Gabriel, however, doesn't, yet the PC is told that this is a Gen 3 Synth.  The evidence shows that this was not a Gen 3 Synth due to the lack of a Synth Component.

Yes this was probably a simple oversight on Bethesda's part, just like the resetting game mechanic making no sense has their handprints all over it.  Still this is going with the in-game world concept of how this could be, and it fits in very well with the prior idea that the Institute is running the entire reset show and, to help out, they have a paid human operative who is given a very simple script to follow when confronted by the Sole Survivor and X6-88.  This Raider group had to be near-by to move in so quickly, and it still doesn't make much sense to look for them if they are well hidden.  Yet this is in keeping with in-world capability and far better than busted game mechanics.  With this line of reasoning the conclusion is that Kellogg was not the ONLY capable high level operative under Institute pay and 'Gabriel' could be given extreme assurances that he will be moved to some other site after the confrontation.  Going with this idea means that Father is using Institute assets to make you feel a part of doing something vital for the Institute. That fits the scenario and the player is set up to 'succeed' not by Bethesda's inability to make a compelling rationale for the Institute, but through the Institute being a seedy place willing to get its way through various means.  Given how the place views people topside as a whole, the expenditure of a Raider gang won't even bother them beyond the loss of some minor assets associated with a higher level field asset or agent.  Synth Retention is not about getting a 'rogue synth' back, but about manipulating the PC into not asking questions and being obedient to the chain of command inside the Institute.

Then there is Roger Warwick, who was kidnapped, tortured and replaced by a programmed Gen 3 Synth to oversee testing a new crop for the Institute.  The quest will have the player going to a few places, but ultimately is supposed to yield a 'happy' Institute outcome of removing any questions about Mr. Warwick having been replaced by a Gen 3 Synth. That is if you play it straight.  Now, if you try to antagonize everyone and get a quite upset farmhand to go back and attack Roger Warwick, well...I have a Gauss Rifle and know how to use it.  Being willing to tank the small arms of the rest of the family is a pretty easy thing to do, and gives just enough time to check the inventory of this synth.  There is something lacking there, however: a Synth Component.  And after running away from the place the family will then turn friendly and allow you to use the workshop...presumably because you showed that Roger Warwick wasn't what he said he was: the husband and father of the family.

So, beyond being yet another oversight by Bethesda...say, if the oversights are fitting a pattern, are they oversights?  If Synth Retention builds doubts then Building a Better Crop just adds to them.  In the computer terminals the PC can find information that Roger Warwick was snatched and, presumably, died or was killed, to put a Gen 3 Synth in his place.  But was he killed?  Everyone associated with the quest in the Institute swears he is, just like Father did with Synth Retention.  Evidence or lack thereof, says otherwise and that Roger Warwick is not a synth.  So just who is this Roger Warwick under the employ of the Institute?  Well I can rule out Gabriel...but after that?  Was Roger Warwick actually replaced or did he become a willing agent of the Institute?  His family could find other Institute evidence or just take the word of the deceased irate farmhand as the truth and come to their senses after the incident.  The simplest way to explain Roger Warwick, and it fits with the general distrust of giving a Gen 3 Synth something other than menial work to do, is to say that Roger Warwick was bribed or otherwise enticed to become an Institute Operative with some minor benefits.  The first crop strain for testing is the Mutfruit that is grown by the Warwicks, and it proves to thrive in the soil of the old sewage treatment plant.  Getting lucky twice would be a bit of a stretch and the Institute would then want to clean up if the second crop also comes out as a success...which if you follow the quest line and do a check-up afterwards, is just the case.

The PC is expected to take the Institute's word on the way things are run and is given scenarios that fit this process.  So where was this guile at University Point?  Or, indeed, any other site that the PC can find Institute Gen 1 and 2 Synths roaming around?  If plugging in the demise of Kellogg is also part of the plan, the creation of an experimental Synth Shaun is part of the plan, and then giving out two missions that shows the Institute to be doing just what it says it is doing while, in fact, running the entire set of encounters via proxy, then all of this must fit into a cogent reason for Father and the future of the Institute.  If Kellogg has proven problematical and divisive within the Institute, mostly for the cyborg parts that extend his life, then who is going to be the capable operative that will express few qualms about working for the Institute?  This person needs to be capable, ruthless and yet able to sell a line of BS to distract others, and generally be able to calm things down when the Institute has operations go wrong.  A bag man.  A new Kellogg.  And to make this person feel even better they will be able to become the new acting Director when Father dies of treatable cancer.

Do we actually get a real funeral for Father if you go down the Institute path?  Because if there is no body going into the ground or being incinerated then the question is: just what happens to an acting Director when they find a good replacement for themselves?  Maybe that is the point to stage a death and become the actual Director, and get shuffled off-stage after a nice, staged death.  It will take a bit for the new person to figure out they are a figurehead and that this Institute they get to work with isn't the real thing but simply a training facility for aspiring managers and a holding pen for those of suspect loyalty.  Actually what is seen is a showplace, meant to overawe and impress outsiders with a staged entrance, and it is a stunning change from the wasteland.  If all that we see is the full entirety of the Institute...well...that is just plain bad game design.  As a functioning operation it makes no sense on the logistics, overhead and maintenance side of things, and better working and far older technology in the Vault-Tec DLC shows just how small in scope the Institute really is by allowing the PC to build something far larger that makes more sense and can actually sustain itself.

What is wrong with the Institute is not the question to ask.  What does the Institute do well?  Now that is the question.  Answer that with lies, deceit, subterfuge, inter-office squabbles, and an ability to stage scenarios to change an individual's mind....then you are on a closer track to the real answer.  For all the beauty of the place, and no detracting from that as it is beautiful, the Institute is not going to change course for anyone, including the PC.  And if that individual can be corrupted, misdirected or made to feel important enough to win them over to the Institute...well...what is the loss of a couple of operatives in the larger scheme of things?  And as for Shaun...is he really your child?  Kellogg and the information you can find shows this to be the case.  Yet, given what can be seen about Gabriel, Roger Warwick, and the methodology of the Institute, the question does have to be asked as material from the Institute and even what you are told is the truth can be demonstrated to be false.  And you are not allowed to ask meaningful questions about past operations of the Institute, either, even after being told that all your questions will be answered.  By not answering them, by misdirecting on missions and generally operating as an authoritarian or totalitarian organization, the questions are answered.  Side with the Institute and you can gleefully slaughter your way through two other factions, and become a willing subordinate in the structure of the Institute.  A subordinate who is given a fancy title and yet not granted a budget nor the means to change policy of the Institute...policies that would need to be changed just to have the Institute survives it will be out of people in a generation or less.  Just as the West Coast Brotherhood will need to change its policies if it is to survive, so to the Institute will have to do so if you go with the Institute ending.  The Brotherhood can see reason, and shown a working example with the East Coast Division.  The Institute?  It is on a high tech death march to redefining mankind and defining itself out of the picture.  If what we see is all there is.

That is a mighty big 'if'.