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I never quite understood the disconnect between the Klingon appearance in the original series and the others (TNG and beyond) until I read recently on Wikipedia:

A canonical explanation for the change [in Klingon appearance] was given in a two-part storyline on Star Trek: Enterprise. The two episodes, "Affliction" and "Divergence", aired in February 2005. An earlier story arc featured the Augments, genetically-engineered humans left over from the Eugenics Wars of the late 20th century, and who were defeated by Captain Jonathan Archer and the Enterprise in Klingon space. The Klingon High Council fears that Starfleet was developing armies of Augments; after gaining access to genetic material from the Augments, the Klingons perform experiments to increase their own intellect and strength. The experiments turn disastrous when a flu strain mutates and becomes a deadly plague that spreads across the Empire, causing physical changes resulting in the afflicted bearing a TOS-era appearance. Dr. Phlox of the Enterprise formulates a cure for the virus, but the physical alterations remain in the populace and are inherited by offspring. Phlox indicated that "someday" the physical alterations could be reversed.

But in the TNG episode "Rightful Heir," the cloned Kahless has the same appearance as the "mutated" Klingons. Kahless lived long before the experiment in the canonical explanation. Is this a plot discontinuity?

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    “A canonical explanation for the change was given in a two-part storyline on Star Trek: Enterprise” — God, it was, wasn’t it? That’s the difference between DS9 and Enterprise. DS9 makes the issue into a funny one-liner for Worf; Enterprise makes it into a damn two-part episode. – Paul D. Waite Jun 27 '11 at 14:01
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    @Paul - You're right, of course; Enterprise took itself too seriously at the best of times. However, "Affliction" and "Divergence" were pretty good episodes, built around a silly premise. – neilfein Nov 18 '11 at 1:46
  • Similar question about Trills: Are there in-universe explanations for how some species' apperances change between series? – user56 Jul 31 '12 at 7:18
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Kahless in "Rightful Heir" had the original, non-mutated appearance (you can see a screen capture on Memory Alpha for confirmation).

Prior to "Affliction" (including the Star Trek: Enterprise pilot, "Broken Bow"), Klingons had the same appearance as they did in TNG and beyond. The idea is that they had appearance A before "Affliction", appearance B until TNG, and went back to appearance A sometime before TNG.

So, Kahless, having existed before the events of "Affliction", was unaffected. However, there is a plot descrepency in the original series episode "The Savage Curtain" where there is apparently an appearance B version of Kahless (again, click into Memory Alpha for confirmation).

But this is retconned to being an approximation of what the appearance B Klingons thought he looked like, not the actual Kahless.

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    Kahless in "The Savage Curtain" was created by aliens from the conceptions of the Enterprise crew; they had the appearance that the crew generally thought of them as, and since they've only been encountering appearance B Klingons... – Izkata Nov 18 '11 at 0:31
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    Now we need to factor in how Discovery complicates that... – Keab42 Feb 13 '18 at 17:19
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One explanation I read (I believe in the Star Trek Encyclopedia) is that the creature from The Savage Curtain created the opponents from Kirk and Spock's imaginations (just as he did their allies), and since Kirk and Spock knew only Klingons of the TOS variety, then that is how they imagined Kahless. Sorry for the lack of sources on this one.

The original Kahless, having lived eons before any series takes place, was therefore of the ridged forehead variety, and his clone remained thus. The thing that's nice with this explanation is that whether or not you consider the Enterprise retconning, it works.

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This is kind of a retcon, or retroactive continuity, where later episodes (or, in this case, a later series in the same canon) alters perviously established facts. In this case, the Enterprise episode retcons the TNG episode in a way that says, what you think you saw -- you didn't.

So, even though the Kahless clone looks like the mutated Klingons, since Enterprise retconed the Klingon story line with new information, he really didn't. Wikipedia has a piece on retcons.

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    But as Mark explains, the TNG Kahless doesn't look like a mutated Klingon. The mutated Klingons are the orange-skinned, no-cranial-ridges, Asian-looking ones. The original Klingons look like Worf and all the other TNG Klingons. – Lèse majesté Nov 20 '11 at 4:59
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I always just read it as Ridges being a prior evolution of Klingon, Unridged being the more evolved form and the virus causing their physical appearance to revert to a less evolved state.

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    Do you have any evidence you could edit in that supports this theory? – TheLethalCarrot Feb 5 at 8:02

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