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Here's a question... when did the cloning process start? What little information we have doesn't provide a date. Cloning was not part of its original mission so we shouldn't assume they started cloning Gary's right after the doors sealed. Either the terminal in the entry in the Citadel about the vault's purpose was a lie or the Cloning process started long after the vault first closed.

They ate them.

Prove its the same clones oh and prove the log wasn't written a year ago.

Ah but look at how it strings together with a couple other vaults.

Vault 87 was retooled for researching FEV

Vault 108 ended up producing clones

Vault 92 tried to use "subliminal suggestion." to program people.

Taken together you have an army of genetically enhanced super soldiers you can grow in lab and program to your heart's content. Of course each experiment was a partial failure

The main power supply was intended to fail after twenty years but that doesn't mean no one could have figured out a way to fix it. Or some contractor saw the error in the power supply design and fixed it without telling anyone.

The Citadel computer on the vault 108 outlines the Vault experiment, which did not include cloning research. In fact it set up an entirely different kind of experiment. So either the terminal entry is a lie in which case none of the information can be trusted including when the MAIN power supply would fail. Or the residents of the vault survived the experiment and fixed the problem before going on to other things.

We also don't know what would be standard equipment in a 2077 medical or science lab.

The Gary's are also listed as being increasingly hostile not unintelligent. Aside from having a language made up entirely of different ways of saying "Gary" they aren't actually any dumber then the random NPC's you encounter in combat.

Hell we don't even know if the cloning experiment was done by the original inhabitants of the vault. Some other group could have laid claim to the abandoned equipment and retooled it for their own purposes.

So what you're saying is education doesn't exist, that one generation can't raise and train the next generation? Maybe you should go criticize the existence of the Enclave in Fallout 2 for doing that exact same thing.

Plenty of things went wrong with the Vault experiments usually to the misfortune of the residents, Vault 13's spare waterchip got sent to a different vault for example.(speaking of which its possible the cloning equipment was shipped to the wrong vault) Its not unreasonable that someone building Vault 108 notice the fault in the main reactor and not knowing it was intentional fixed the problem. OR that the residents fixed it themselves.

How do you know what equipment is required? YOU DON'T how do you know that the equipment couldn't be modified from something else. YOU DON'T. Vaults are supposed to have population control, they recycle waste, grow their own food all these things to make them completely self sufficient for decades or even over a century.

A medical lab capable of growing clone organs as donations would be in short supply isn't unreasonable standard equipment.

The Enclave was stuck in isolation on an oil rig for a century before they ventured out to explore the wasteland. So they were stuck in in their own vault long after most others had either failed or opened to the wasteland.

Wait, Pip - Boys are permanent? Why?

Pip-Boys aren't permanent. But Gary 23's Pip-Boy (and I think every Pip-Boy of F3's) is permanent, because the Outcasts cut off his arm to get this interfering device for the Anchorage sim - doesn't make sense otherwise. I tried to also put an explanation for this into the theory. Plus for the jet in pre-war facilities.

No Pip-boy is permanent, it is however suggested it is bio-metrically locked, so the user him/herself would have to take it off, or they would need very specific Pip-boy unlocking tools/knowledge.

The Gary clones are too stupid to remove it themselves, and the outcasts wouldn't have the tools to do it correctly, so cutting of his arm would be the only way.

If it's biometrically locked, the Outcasts could have circumvented the problem (simply coercing the clone to do what they want, unless they don't know how it's locked, which isn't plausible for a tech crazy faction).

You can't "make" or "coerce" Gary clones into anything, they are mindless and violent.

And its entirely possible they dont know how its locked because the BoS deals mainly in weapons tech, not Pip boys, which incredibly few people in the wastes actually have. Knowing a lot about guns doesn't make one a robotics expert.

They have dealt with people with the pipboy 2000, entirely different model, that isn't biometricly sealed.

Lyons likely left before the BoS moved into the Vegas area, and there's all of about what? 5 people outside vault in Fallout 3 that actually has a pipboy?

is it possible Lyons died from natural causes as old as he was?