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On the Matrix wiki, there's an article about the Nightmare Matrix which says:

The Nightmare Matrix was the second prototype Matrix, designed by The Architect after the massive failure of the Paradise Matrix in the hope that human minds would more readily accept an imperfect world with suffering. Unlike the first version, this Matrix instituted a basic cause-and-effect programming and forcibly made those connected to it accept the program.

Vamp Prime, a possible remnant of the Nightmare Matrix. It also featured programs that resembled mythical evil creatures in various human mythologies such as vampires, werewolves, zombies, aliens, etc. It also failed, but many of the programs who were designed for it survived deletion in exile.

The Merovingian and his wife, Persephone may have had their roots in this version of the Matrix. Upon its failure, the Merovingian started a smuggling ring of programs and information to provide a haven for exiles that would last for 6 cycles in the final version of the Matrix.

The Nightmare Matrix is also featured in the Matrix Online.

But like many articles on the Matrix wiki, it doesn't really give any specific references that would allow readers to verify what it says. The only evidence I know of is this bit of dialogue from Persephone in The Matrix Reloaded, right before she shoots the Lupines Cain and Abel:

They come from a much older version of the Matrix, but like so many back then, they caused more problems than they solved. My husband saved them because they're notoriously difficult to terminate. How many people keep silver bullets in their gun?

Does anyone know exactly what was "featured in the Matrix Online" (or any other published sources like comic books)? Did they explicitly use the words "Nightmare Matrix", or specifically say that programs with "supernatural" characteristics, like the ghost-like Twins or the Lupines and Vamps, came from the second iteration of the Matrix after the original Paradise Matrix which was mentioned by the Architect (though he didn't use that exact term)? And even if there was a Matrix with many "supernatural" programs, do we know that this version was especially "nightmarish" for inhabitants, as opposed to these programs just showing up rarely and possibly playing a similar role to Agents in the later versions of the Matrix? Finally, is there evidence for the idea that the second version of the Matrix was the first to institute cause-and-effect, and that this was the reason for the Merovingian's emphasis on the idea, as opposed to it just being his personal philosophy to emphasize cause and effect over choice?

Edited to add: Richard mentions there was nothing about this in the Matrix comics, and it wasn't in the Animatrix either, so I think that just leaves The Matrix Online for a source...I know that monstrous programs like vampires were featured, does anyone know if anything further was ever revealed about their background, as there was with Seraph according to the "Online" section of his wikipedia article? Or about the origin of the Merovingian's fixation on cause and effect?

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    To my knowledge, there's no reference to the "nightmare matrix" in any of the web comics. – Valorum Jul 17 '15 at 17:12
  • @Richard I don't know of any reference to it, either. I doubt there'd be one, though -- they mostly (all?) take place before Neo visited the Architect and found out about the Nightmare Matrix. – Null Jul 17 '15 at 17:29
  • @null - Several are set after Neo's death, notably I Kant. No help there, though. – Valorum Jul 17 '15 at 17:37
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    Regarding the Merovingian's fixation on cause and effect, my answer to a question about him covers that. Basically, he was replaced by the Oracle because he doesn't understand choice, so he's bitter about it and claims that there is no choice (only causality). – Null Jul 17 '15 at 20:51
  • @Null - It's an interesting theory but there's no canon evidence whatsoever to back it up, only a quote from the mxo mythos files – Valorum Nov 30 '15 at 11:33
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With regards to The Matrix Online, the references to the prior "Nightmare" version of the Matrix was within the Ashencourte and Widow's Moor Constructs. In the game, constructs were special areas that held archived versions of the Matrix. In the the cases of the two above mentioned constructs the setting was Gothic, and they were populated with various vampire and gargoyle types of enemies.

  • That seems like good evidence for a prior version of the Matrix that featured more extensive magical/fantasy settings (as opposed to my speculation in the comments that supernatural creatures may just have been Agents from a previous version)...it still doesn't prove definitively this was from the second Matrix, but that seems pretty likely given the Architect's comments cited by Richard, so I'll accept this as the best evidence we're likely to get. – Hypnosifl Nov 30 '15 at 19:07
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The primary reference seems to be the Architect's speech, wherein he explicitly confirms the existence of a "paradise" version of the Matrix as well as a "Nightmare" version

Architect: The first matrix I designed was quite naturally perfect, it was a work of art, flawless, sublime. A triumph equalled only by its monumental failure. The inevitability of its doom is as apparent to me now as a consequence of the imperfection inherent in every human being, thus I redesigned it based on your history to more accurately reflect the varying grotesqueries of your nature. However, I was again frustrated by failure. I have since come to understand that the answer eluded me because it required a lesser mind, or perhaps a mind less bound by the parameters of perfection.

The later arrival of various demonic creatures; ghosts, werewolves and vampires would seem to strongly confirm the nature of this Matrix, a living hell populated by monsters.

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    Good point, that could be where fans got the idea. But arguably the current iteration of The Matrix still reflects "the varying grotesqueries" of human nature, like war, crime, poverty, etc. Isn't it possible the second version the Architect talks about was just a reasonably accurate historical simulation like the one we see, except lacking the element of humans being given a choice to escape to Zion? I wonder if anything more definitive was presented in The Matrix Online. – Hypnosifl Jul 17 '15 at 17:14
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    @Hypnosifl But then why were the "supernatural" programs exiled? – Null Jul 17 '15 at 17:29
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    @Hypnosifl - I think the implication of his speech is that the second iteration was grotesque in itself. He'd tried happy, now he was trying sad. – Valorum Jul 17 '15 at 17:39
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    @Richard - Wouldn't it have made more sense for him to say something like "varying grotesqueries of the human imagination" in that case, rather than "of human nature"? "Grotesqueries of human nature" seems more like it's talking about the bad things real humans do to each other, on an individual level and also in terms of the structure of society (differences in power and wealth for example). – Hypnosifl Jul 17 '15 at 18:55
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    Don't remember where I saw it - some forum or something - but someone posited the theory that the 2nd matrix had TOO much freedom, dynamically building itself based on the people inside it. The theory was that the supernatural programs were based on the imagination of the people inside the Matrix itself, and that it failed because the monster programs were killing off too many people to make it viable long-term. A fan theory, but an interesting one. That was years ago so it was probably on Usenet or a newsgroup. – Omegacron Jul 17 '15 at 20:46

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