Ok so I'm going to try to avoid spoiling anything here but it's an interesting issue with Fallout 4 Super Mutants and it does involve a few minor spoilers. But I'll try to avoid them.

Anyway.

So there's a part in the main quest where you come across 3 super mutants in the buff in a lab.

And what you see is that these Super Mutants are completely smooth. Nothing. Like Ken dolls. Now this is an odd development and one that you'd be right to ask "well why should we care?" But this does go against pretty much everything we know about Super Mutants from previous games.

The FEV virus (either the Vault 87 stain or the Mariposa Strain) mutated the hell out of it's victims, building tons of extra muscle and bone and constantly repairing the body's cells. This made them all sterile though as the virus hit the victim's gametes and "repaired them". BUT it didn't really change anything else. So Super Mutants still had their primary sixual characteristics (ie: anything you have before puberty hits) and were still able to have six. Fallout 2 gets pretty explicit about this with a married super mutant couple and one super mutant who makes the PC his "special friend" for the night if you lose an arm wrestling game to him. I won't go into any detail on that one, but you wake up the next day with a ball gag in your inventory as a momento. So yeah...use your imagination there.

The loss of secondary sixual characteristics seems to be more the result of the sudden gain in muscle mass and mild levels of mutation than a "androgynizing" agent in the virus.

So then, why to those 3 Super Mutants not have anything below the belt in Fallout 4? Is it a screw-up on the developer's end? Were they meant to be in loincloths but they were forgotten and we just got the generic non-explicit, no-genital body model that all characters in the game use? Or is something else going on here?

In the Brotherhood's records you come across they say that the super mutants in the common wealth are quite different from those in the Capital Wasteland.

. And If any of that's the case, why do the super mutants randomly comment on how they're trying to find more "green stuff" ie: FEV?

It's very confusing.

Then, with the above, you have Virgil, who ends up "restored" thanks to a very specific vial taken from the Institute.

Yeah, I'm still trying to wrap my head around the Super Mutant take. It seems odd they're everywhere in the Commonwealth, and I haven't found (in my game) a reason for this.

You should probably replay Fallout 3

http://fallout.gamepedia.com/Vault_87_terminal_entries

Vault 87 FEV has always removed gender specific features as part of how it works.

the FEV probably removed reproductive capabilities from their test subjects to make them have less testosterone and to keep them in a calm state without modivation to escape as they are infact giant hulking monsters that can rip a building apart if they have enough modivation

So, yes, the Super Mutants of the Commonwealth are creations of the Institute's modified FEV. As for where all of those hundreds and hundreds of mutants come from... well, it's heavily implied that people who are replaced with synths become the FEV test subjects, and a whole lot of people have been replaced throughout the decades. Presumably they also left vats of FEV around surface-side to see how well the experimental FEV works in the "real world," rather than in a controlled lab environment.

The only explanation I've found online for the sheer number of Super Mutants in Fallout 4 (which is absurdly high even if you pretend re-spawning doesn't happen) is that

.

But then that doesn't explain the amount of super mutants we see, or why they're all genderless.

This is a fair point as well. East coast Super Mutants aren't the same as the Super Mutants created for the Master's army. They both use the FEV, but presumably there were different strains being tested. And/or the Master undid the asixuality in an attempt to create an army that could procreate. He wanted to turn everyone into Super Mutants, after all - and that includes outbreeding as well as vat dipping.

Very little about the Commonwealth super-mutants and the FEV plot makes sense. And even less is explained.

It was haphazardly shoe-horned in for no reason.

That being said. The FEV-87 strain leaves those that are dipped in an assixual state. Unlike those of the Mariposa Strain. So presumably the FEV-Institute strain is based on, or somehow related, to the FEV-87 virus.

However, its also never explained where Bioscience got the virus from in the first place. So it may just be a coincidence.

Given that, previously, only the Vault 87 strain of FEV was known to create behemoths.... that seems unlikely.

I already explained it, it makes perfect sense why they would do that to their test subjects. They don't want their subjects they are testing on and letting wander the halls to get excited and kill someone

Perhaps. But the source of the Institute FEV is left purposefully vague. So we can't be sure.

That wasn't what I was referring to.

Good catch there. Though I'll argue that the claim that the line "losing most of their visible female indicators and transforming to an almost asixual state" can go either way. If they are losing all of their secondary sixual characteristics the statement would still be valid. The line is "losing MOST" not all. But it could also indicate that they were going completely asixual as well.

But then where does the statement from the Prydwen terminals about the super mutants in the Commonwealth being very different from their DC cousins come in? I think it's an indication of the 100% asixual nature of the Commonwealth Super Mutants.

They are different externally and internally, but that doesn't change the fact that both the vault 87, and commonwealth, super mutants had no gender specific sixual organs at all.

http://fallout.gamepedia.com/Vault_87_super_mutant#cite_note-FO3OGGGYE-1

Fallout 3 Official Game Guide Game of the Year Edition p.42: "Super Mutants"

"The Super Mutants that infest the urban ruin of Washington D.C. originated in Vault 87. Those unlucky enough to have reserved space in Vault 87 soon found themselves forcefully taken to a secure part of the vault, where they were locked in airtight chambers and exposed to a concentrated form of the F.E.V. The Overseer and his security force had no real idea what to expect; they were simply following the "plan." When the exposed vault dwellers started transforming into Super Mutants, nearly the entire vault population had been exposed. Those who hadn't yet metamorphosed knew what was coming, and, well...it didn't end well for humanity.

The dwellers of Vault 87 were turned into Super Mutants in 2078, and have been a presence in the Capital Wasteland ever since. Most of those original Super Mutants have long since been killed. But whether it's because of the nature of the F.E.V. they were exposed to, or a simple underlying human instinct, the Super Mutants of the Capital Wasteland are obsessed with the preservation of their own species. Super Mutants are asixual and incapable of procreation, so their only way of reproducing is to kidnap other humans, drag them back to the Vault 87 chambers, and infect them with F.E.V. And so they have done, for nearly 200 years.

Super Mutant society is loosely hierarchical, with the weaker (most recently transformed) Super Mutants generally giving way to the stronger. The Super Mutant hierarchy, as defined by the Capital Wasteland contingent of the Brotherhood of Steel, is as follows: Grunt, Brute, Master, and Behemoth. Generally speaking, the Super Mutants of the Capital Wasteland get bigger, stronger, and dumber as they age. The Behemoths are so strong and savage that they’re the only thing feared by the other Super Mutants."

That's something I missed in Fallout 3. Then again, I really hated the layout and design of vault 87 when I was playing Fallout 3.

So then the official explanation is that the vault 87 strain makes it's victim's completely asixual. It's odd but I can roll with that.

I really hope that they focus on the super mutants in a DLC though as there's nothing I've come across in the game so far that explains why there are so many super mutants in the commonwealth or where the institute got it's sample of FEV from. The virus wasn't a common thing before the war. It was really a last ditch attempt to counter the threat of nuclear war by turning the entire army into radiation proof, super intelligent mini-hulks. But it never got beyond the "unethical human experimentation in secret labs" point.

You can have bondage six with Fallout 2 super mutant.