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Jung tells us that the feminine aspect of Mercurius is represented by Melusina, here shown in 'Melusine's secret discovered', from Le Roman de Mélusine by Jean d'Arras, ca 1450-1500. She corresponds to the female Nous, and to the Edem of the Gnostics.[a] [Image from the Wikipedia 'Melusine' page, public domain, via Wikimedia Commons.]
As quoted from Jung's Psychology and Alchemy in part 36 of this analysis, it is Mercurius who "stands at the beginning and end of the [alchemical] work."[b] (Note that this implies that in Mercurius, we have a link between the rubedo, the end of work, and the nigredo, its beginning.) Jung dedicates an entire section of his Alchemical Studies to explaining the nature of Mercurius. Jung associates Mercurius with quicksilver and/or water, fire, and spirit and soul. To the alchemist, he is the transformative substance itself; as such, he is "obviously a projection of the unconscious." He "consists of all conceivable opposites", and is thus a duality; but, he is also a unity, and he has a triadic nature as well. He is also the prima materia itself. He "represents on the one hand the self and on the other hand the individuation process and, because of the limitless number of his names, also the collective unconscious."[c]
The foregoing is by no means an exhaustive description of Mercurius, but it's enough for our purposes at the moment. Mercurius is alluded to in 2001 symbolically by, for example, the black monolith, which is associated with the nigredo (the beginning of the alchemical work). Speaking more generally, since A Space Odyssey depicts the Magnum Opus itself (as described earlier in the analysis), and since Mercurius represents this (the alchemical process), the entire movie could be said to suggest the 'presence' of Mercurius.
Basically, the alien individual, consisting of pure energy, has been storing itself in Discovery One's electrical/electronic circuitry during the Jupiter mission. This individual (the same one which previously occupied Heywood Floyd's body), wants to unite its femininity (recall the blue symbolism), Melusina (also called Melusine), with Bowman, who in turn represents the active and masculine half of Mercurius.[d] It is necessary for the alien's becoming Mercurius, who is a union of all opposites, that the 'good' Jew, Bowman, unite with the 'bad' Jew, HAL. (In Jungian terms, when Bowman does this, he will have assimilated his own psychological shadow.) Bowman's assimilation of evil when he defeats HAL, is to be followed by the alien infusing Bowman's body while he's watching Floyd speak on Discovery One's video monitor (in HAL's logic/memory compartment) near the end of the movie. This is then to be followed by Bowman's return to Earth, then his death, so that the alien/Bowman combination can be reborn as Mercurius When the alien accomplishes this, the resultant being (i.e., the being that constitutes the fetus shown at the end of the film) is the aforementioned union of all opposites: feminine and masculine/yin and yang, good and evil, man and machine, pure energy as well as physical body, etc.
The alien intentionally planted the monolith on Earth such that it is 'distorted', for as previously explained, it is rectangular instead of square, symbolizing its incorporation of an over-emphasis on the unconscious, which is feminine in character. The (distorted) monolith is planted so that man's ancestors, under the influence of the alien race 'via' the presence of the monolith, will discover how to use weapons, and thus, humanity will be put on the path to its own self-destruction. Humanity's history is to include a 'weeding-out' process by which a suitable specimen is to be found, with whom the alien can unite to achieve its perfect being. It turns out that Bowman is this specimen.
The alien, which has been storing itself in Discovery One's circuitry during the Jupiter mission, begins to combine with Bowman (above left) while he is viewing a prerecorded briefing from Heywood Floyd (above right) after he has disconnected HAL (recall that the alien had earlier occupied Floyd's body).
The alien's becoming Mercurius is its 'plan B' of sorts. The original plan was for the alien and HAL, to share in the benefit which was to be obtained by defeating Bowman and Poole, and fooling everyone on Earth with the faked mission broadcast. As will be explained later in the analysis, this benefit was to be the ruling over of a kind of evil kingdom by the entities that HAL and the alien represent, respectively. The original plan for the three astronauts who were in hibernation, was for them to be revived by HAL, and to then aid HAL and the alien by providing the physical means to move the monolith to its final destination. The alien starts out abetting HAL, by helping with the events surrounding the attack on Poole: The alien makes Bowman forget to put on his space helmet when he leaves the ship to retrieve Poole; and, as will be explained later in the analysis, the alien makes things so that Bowman and Poole do not notice anything unusual when Discovery one is steered off course by HAL.
Originally, the death of Poole was to be followed by Bowman being unable to re-enter Discovery One. When the alien realized that HAL killed the three astronauts who were in hibernation aboard the ship, while Bowman was out in his EVA pod, it knew HAL was trying to cheat it out of sharing in the aforementioned evil kingdom, so it ensured that Bowman decided to enter the ship (through the emergency airlock), so that he could defeat (and assimilate) HAL.
The being shown (in the fetal stage) at the film's ending, is a union of all opposites.
a. Jung, C.G. The Collected Works of C.G. Jung, Vol. 12. Princeton University Press, 1968. para. 404.
b. Jung, C.G. The Collected Works of C.G. Jung, Vol. 13. Princeton University Press, 1970. para. 427.
c. Ibid., paras. 259, 284.
d. As we will see later in the analysis, the alien has actually 'set up' a 'situation' within Bowman's psyche, such that he will see the need to unite with the alien.