I think The Prisoner was all about cloning.

“The Prisoner” is an allegory, so any attempt to interpret it literally will never fully make sense. If we insist on taking a stab at it, though, and if we pretend there was a “Grand Design” for the whole franchise (Which there clearly wasn’t), then I have a theory.
I think #6 was a replicant.
Or clone or whatever you want to call it. Think about it: The Village had much higher technology than the 1968 world. Higher than we have today, actually. They could resurrect the dead, and they definitely had full-grown-adult-clone-with-memories technology. We see it in the very first episode. We also see clones of #6 on two separate occasions: #1 himself is a clone (50 year old spoiler. Sorry.) and in “The Schizoid Man,” they bring in another one, who’s also a secret agent, as part of a convoluted and largely nonsensical plan to make #6 question his identity.
Unlike ANY of the other prisoners (up to and including the various #2s), they are not allowed to harm 6 physically or mentally. They want him broken, not damaged. Allegedly they want him to tell them why he resigned, but that never made much sense, as in the beginning of every episode we see him hand-delivering a letter that clearly says, “My resignation,” so really they already know. In the first episode, #2 even says, “Personally, I believe your story. Things have come to a pretty bad pass when a fellow can’t just chuck off a job because he wants to. But they like to be sure…”
Then there’s the opening narration:
“You are #2”
“Who is #1?”
“You are #6.”
By the last half of the series, the delivery on this has changed:
“Who is #1?”
“You are, #6.”
Of course by then we’ve stopped really paying attention to the opening, and no longer really notice it.
In the finale, it turns out that the Village is in a constitutional crisis, and need a new leader. #6, having weathered every trial, is to be that leader. In our brief meeting, #1 is clearly insane: he’s wearing a mask, with another mask under that (An ape), and his real face under that, gibbering like a lunatic.
So really the whole story here is that the Village needed a new leader, and only John Drake/#6 is fit to do it, for whatever reason. They tested him to beyond the breaking point (God knows how many other 6s they tried, and failed with) before finding one with the unyielding will they needed. And of course he immediately picks up a machine gun and kills them all.
I’m going to take this a bit further. #6 is clearly John Drake, the protagonist of the TV show, “Secret Agent,” and the other spy show, “Danger Man,” prior to that. There’s the unintentionally foreshadowing line in the “Secret Agent” theme, “They’ve given you a number and taken away your name.” However, there are some continuity errors in character between the two “Drake” series. Specifically, in “Danger Man.” Drake is American. In “Secret Agent,” he’s British.
My take on this? “Secret Agent” Drake is a clone of “Danger Man” Drake. Even “Secret Agent” Drake may not be the first. In the opening narration of every episode of “Danger Man,” Drake says, “the job falls to me, or someone like me.” There’s a vague implication that The Village has been around since the war. Assuming it can only be run by a John Drake for whatever reason, the original would have been in his 30s back in the 40s. So they clone Drake Prime, give his replicants fake memories (In the penultimate episode of The Prisoner, #2 seems to already know all about Drake’s life before Drake tells him), and different names and then send them out as spies to mostly get killed off by attrition (Evolution in action!) When the reigning #6 starts to break down or wear out or whatever, they start bringing in the more successful clones and testing them. Whichever one doesn’t break is the new #1.
That’s my longwinded theory. What do you think?

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