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Xenogears in comparison to Christian prophecy. (Big Spoilers)
Forget that Deus means God, although I'll come back to that.
Alright this is pretty much a good vs. evil / God vs. Satan comparison made through the linking of major historic/prophetic events in the Bible and the events of Xenogears.
The Wave Existence is of a higher dimension, which I will compare to what is essentially God. Deus is Satan. Through both the Wave Existence and Deus humans are created. This statement takes a bit of explaining. . . if humans were created through the wave existence alone, they would be pure (one-dimensional), think back to the Garden of Eden. Because of Deus, there is a struggle between good and evil, such as the struggle initialized by the temptation of the snake (Satan, again). I think we can agree on this since it is the conflict of the game, which isn't really presented until the end, but what I am getting at is that through God and Satan (or W.E. and Deus) humans, as beings that struggle with good and evil, were created.
A more self-explanatory comparison between the two is the analogy of Fei/Lacan/Abel as Jesus. Fei, in a sense, is the three-dimensional form of the Wave Existence, just as Jesus is of God. He eventually reincarnates as Fei, and as was his destiny, proceeds to eliminate Deus. I think you can draw the connections here.
Yeah, Xenogears offers an immeasurable amount of modifications to this story, as does the Bible, but I believe the frameworks are the same.
The Wave Existence always struck me as a bit weak and selfish. Certainly not godlike.
"You must not worship or serve any idol, because I, the Lord your God, am a jealous God. If you hate me, I will punish your children, and even your grandchildren and great-grandchildren. But I show kindness to thousands who love me and obey my commands." Ex 20.5-6.
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I see the game more in terms of a comparison with Gnosticism.
I cannot compare Satan to Deus without mentioning the Demiurge as well. (http://en.wikipedia.org/wiki/Demiurge#Gnosticism) (http://i35.tinypic.com/2ze05jd.jpg). In the Gnostic tradition, Sophia is the final emanation of God, and she creates materiality, souls, and the god of the material world, the Demiurge, by engaging in a creative act with only herself (http://en.wikipedia.org/wiki/Sophia_(wisdom)#In_Gnosticism). Similarly, Elly bears humankind without any apparent sexual intercourse, or male DNA information as it would be. Sophia completes the syzygy pair with Jesus, the bringer of divine knowledge, himself being an allegory for all prophetic wisdom (http://en.wikipedia.org/wiki/Syzygy) (http://en.wikipedia.org/wiki/Jesus#Other_early_views). Similarly, the Contact is the only human who is able to make contact with the divine. Also, both Sophia and Jesus are emanations of the One God, just as Elly is created by and Abel is empowered by the Wave Existence, allowing him to start a new life on an uninhabited planet.
More importantly, there are several similarities between the Demiuge and Satan, one of which is their depiction as serpents. Both have been represented as the antithesis of God, which is impotence, non-presence, ignorance, and belligerence. (http://en.wikipedia.org/wiki/Demiurge#Samael). Both have also been represented as demi-gods and controllers of the human world. (http://en.wikipedia.org/wiki/Satan#In_Christianity). Neither is actually the creator of the universe which they control and believe is their own. Rather, they and the universe were created by divinity.
In taking the Demiurge as analogous with Deus, we must take it to also be analogous with Miang, humanity's supervisor. As I pointed out in the first set of links above, both the Demiurge and Miang ultimately have the form of a chimeric snake, except that the Demiurge has the head of a lion and Miang has her own head, which is actually Elly's at that point. Notably though, Elly is associated with the cusp between the astrological signs of Leo and Virgo. Her gear is, after all, called Vierge and her Omnigear goes by Rergs, which is a mistransliteration of Regulus, the Alpha star of the Leo Constellation. Apparently, the Earth makes its closest approach to this star on August 23, the last day of Leo or the first day of Virgo which is the cusp between the signs (http://en.wikipedia.org/wiki/Regulus) (http://en.wikipedia.org/wiki/Leo_(astrology). Furthering the snake imagery, Miang's gear is called the opiomorph and her final form is called Urobolos (http://en.wikipedia.org/wiki/Ouroboros). Deus/Miang adheres to this symbolism by absorbing its own offspring, which is basically the totality of humanity. Interestingly, Jung writes that the Ouroboros is indicative of a 'feed-back' method of creation (http://en.wikipedia.org/wiki/Ouroboros#Alchemy). In Xenogears, Elly is created by the Wave Existence from Fei's desire and Deus' form and she represents Abel's mother and lover, but she bears all of humanity, which will then bear the Contact and the Antitype again.
I believe the game has a more complex dynamic than good vs. evil. If anything, I think the game is about knowledge vs. uncertainty. To a certain extent, the greatest ambiguity in the game is whether or not the Wave Existence is truly of divine origin, as it shares as many similarities with the Demiurge as Deus does. The Wave Existence resides in the four-dimensional world, after all. If it is truly of divinity, how does it get trapped by something that is clearly man-made, thus profane i.e. not divine or sacred. However, it still exists and is powerful enough to create a human and to empower Abel. Because the Wave Existence fulfills Abel's unconscious desires, or those desires which are most often associated with the Id and one's base need for nurturing and a home, I believe it is relevant to point out that Jung states of the man's relationship with the Ouroborus that "[it] constitutes the secret of the prima materia which unquestionably stems from man's unconscious." So, rather than the Wave Existence being divine, it simply represents a bit of the "light" which was created by God to fill the void and so Fei's contact with it is nothing more than him reconciling with his unconscious desires. It is further worth noting that Fei speaks to the Wave Existence only after coming to terms with his original personas, one of whom is named Id.
I believe that the comparison between the Wave Existence and the Demiurge is most complete with the transmogrification of Krelian into the Wave Existence. (http://i35.tinypic.com/2ze05jd.jpg). Krelian, as a scientist, is the ultimate representation of uncertainty and the derivative nature of creative processes. He continually denies his human inferiority and strives for Godhood, despite being totally ignorant of the eventual outcome. Ultimately this might just reveal my bias toward religion in wanting to assert that there is no God in Xenogears, but only uncertainty.
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Haha thanks for taking it that step, or multiple steps, further.
Fidormula -- "You were too busy being immortal."
That was fun. Give me more.