Where do you get that his "real" name is Carl? If The Prisoner (#6) has a "real" name, it's John Drake, (ie, Secret Agent, aka Danger Man, from which Patrick McGoohan first starred.) In fact, the photo used of #6 in The Village is a stock photo of "John Drake" from Secret Agent. However, I have never heard of #6 being referred to as "Carl", even by his fiance. I just re-watched "Do Not Forsake Me Oh My Darling" (the episode with Janet, #6's fiance) and she never once utters "Carl."
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Please, if you can, point to your reference where #6's name is Carl.
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Also, if you wish to speak of running order, you should check out the Wiki of:
http://en.wikipedia.org/wiki/List_of_The_Prisoner_episodes
There are 5 different running orders listed, all of which seem to have their own validity.
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In the end, Patrick McGoohan (RIP) should have the last say in all of this... and over the years he never once admitted that #6 was John Drake, (or any other "real" name). Plus, he always said that the running order should have been much shorter than it was: only 7 episodes:
Arrival
Dance of the Dead
Free For All
Checkmate
Chimes of Big Ben
Once Upon a Time
Fallout
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The reason the series lasted 17 was due to network requests, not Patrick's. Although British TV series have always been "odd" in the number of episodes making a whole "season," they didn't want to do just 7 episodes, but Patrick didn't want to do 24... so, there are 17.
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As for the running order debates... frankly I don't care where AB&C, and The General belong in the greater running order, but they certainly belong in That order, (and back to back). Colin Gordon is one of the few actors who plays #2 twice, and in the opening sequence of the episode of The General he says "I AM Number 2" NOT "I am the New Number 2." Thus bridging his appearance from AB&C into The General. If we are to take The General as coming before AB&C, then it's rather out of place to then hear him say he is the New #2 at the start of AB&C.
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Another running order debate is with placing Checkmate before Free For All. Frankly, Free For All MUST come before Checkmate. In Free For All, as he is campaigning for #2's "office" he announces that he intends to find out who are the prisoners and who are the warders. Then, in Checkmate he formulates a theory on which to test this separation. It would seem illogical to reverse these two in the running order.
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And... no matter where you place Dance of the Dead, it must be within the first 2 or 3 episodes as one of #6's opening lines in that episode is "I"m new here!" If this episode starts creeping into a running order later that the 3rd episode, that line becomes less logical.
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As for the second-half (or last third) of the running order... there really aren't as many line specific instances, or continuity points to really say one way or the other. Maybe because these later episodes were merely filler... until we get to the conclusion with Once Upon A Time and Fallout, which (frankly) should be watched as one episode.
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If it were me, this would be the definitive running order: (A slightly modified Six of 1 Appreciation Society running order):
Arrival
Dance of the Dead
Free For All
Checkmate
Chimes of Big Ben
AB&C
The General
The Schizoid Man
Many Happy Returns
It's Your Funeral
Change of Mind
Hammer Into Anvil
Do Not Forsake Me Oh My Darling
Living In Harmony
The Girl Who Was Death
Once Upon A Time
Fallout
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Still.... I'd really like to know where "Carl" came from. In my 16 years of fandom with this show, I've Never heard "Carl" being used as #6's real name... in any circles of fans or critics.