I don't think gamesas ever gave a reason. They also can't come from V87 anymore as when you go there it says the tanks are empty....

[Lyons] discovered this abandoned Pentagon military complex. The presence of Super Mutants sent a chill up the collective spine of the Brotherhood; these
weren't the children of the dreaded Master, nor were they the remnants of the band that fled east and were ultimately destroyed (or assimilated into the Brotherhood of Steel) in the Chicago area. No, this was a new breed of Super Mutant, one with a local origin . But where did they come from? What did they want? How were they reproducing? Elder Lyons was ordered to discover the source of this new Super Mutant infestation and wipe it from the face of the Earth.

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.

Sneak or use a Stealth boy to approach the bottom of the steps and eavesdrop on two of them. They plan to search for more of the "green stuff" and use it to make more Super Mutants. Apparently, there is F.E.V. in this facility, and the Super Mutants are using it to reproduce.

All super mutants in FO3 are from Vault 87. The tanks got empty very recently, just before the Lone Wanderer reaches the vault.


This is what the official guide says:

ausir to save the day