That episode ("Chronophasia") really pissed me off because, unlike the other episodes which have a clear solution to the visual puzzle, this one has no answer. I watched it 3 times thinking I could key in on some subtle clues, recurring images, symbolism, but found none. In frustration I turned on the commentary to get the answer, and guess what... They admit it's the one episode that has no specific meaning. Peter Chung even apologizes, saying people have been waiting all these years for the answer but he can't offer anything.
According to him, the original idea was that Aeon keeps waking up from a recurring nightmare covered in blood. Each time she witnesses someone getting killed but not knowing who the killer is. By process of elimination, at the end she realizes the killer is the only person left alive: herself. It was a way of confronting her guilt and the consequences of her violence. That would've been a kickass episode, but as usual MTV censored it (too much blood, so instead of blood she awakens in a pool of meaningless grey goo) and told them to make the story more linear (no more recurring nightmare), and after being tossed to a different writer altogether, the result is the pointless acid trip that we all saw.
Yes there is still a degree of continuity and a bit of a plot to hold it together, but it's pretty devoid of the deeper themes, philosophy and mathematical precision we've come to expect in the other episodes. All the writer could offer as an explanation is "it's about making choices and nothing is real so don't take anything literally." Peter Chung basically grunted and talked about the animation. I think it's clear that his original concept was completely demolished.
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