Baltar as Cylon speculation
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For Gaius Baltar to survive the destruction of Caprica was no small matter, especially considering he is in the wake a nuclear shock wave and that the body of Six that is apparently destroyed in trying to protect him in the events of the Miniseries.
A nuclear blast's shock wave is substantial (not unlike that from a pyroclastic cloud). The shock wave would contain rocks, glass, metal, and other large debris that would bludgeon, pierce and lacerate human tissue with ease and at terrific speeds (at maximum, 1200 KPH, or 745 MPH). Such a debris-filled shock wave would obliterate Baltar's home and easily annihilate Six's body, which at those speeds would provide essentially no protection for Baltar. (For comparison, note that, despite his superior strength, the head of the first Leoben Conoy copy encountered is bludgeoned by Commander Adama with a flashlight, and that humanoid Cylon copies can be shot or killed as easily as a human.) However, it has to be kept in mind that the blast wave had dissipated greatly by the time it reaches Baltar's house some 26 seconds after the detonation that almost blinds him, maybe no more than hurricane force .
Even if Baltar survived momentarily from Six's protection, either the remains of his home would collapse over him, likely trapping him if not killing him, or he and Six's body would also be carried away by the shock wave for some distance. Could the Baltar on Galactica therefore, in fact, a humanoid Cylon?
The "Many Copies" Theory
Humanoid Cylons are designed to be archetypes of human psyche. Biologically, they are not and have never been actual humans.
One notable question would be why Six spends so much time talking to Baltar and then throws herself in front of the blast if she intends for him to die? If Baltar is already a Cylon, his consciousness from that moment would be thrown into a waking duplicate, already disheveled and scraped, where Baltar would merely think he was blown clear to safety where he could run to escape attacks with other survivors. Also, since Baltar appears to be a key in many Cylon plans, they would want to ensure that Baltar would reach any remaining humans to spy for them, and having only one copy might risk the success of such plans. Further, it is the psyche of Baltar that the Cylons may treasure most; few others in the Colonies may have the level of intelligence, arrogance, and neurosis that Baltar has that could prove as easily exploitable. The guise of the great Baltar gives the Cylons a huge natural tactical advantage in that he is well known and allowed access to almost any critical battlestar location. Baltar's slick personality aids him with better finesse and stronger charisma than any humanoid Cylon personality yet seen.
Later events in the series appear to discount this notion of an elaborate plan to save Baltar. In "Downloaded", the Cylons are unaware that Baltar has survived, having received this information from the resurrected Sharon Valerii.
The Baltar-as-Father Argument
Six states her desire to have a child with Baltar. Humanoid Cylon couplings have failed to result in offspring prior to that point (The Farm). If Baltar and Six were both Cylons, it is likely that offspring would either be impossible or at least exceptionally unlikely. This point gives evidence against the Baltar-as-Cylon theory, but Six has repeatedly made it clear that she considers the hybrid human-Cylon baby that Sharon is carrying to be "our" (as she puts it) baby. "Our" may in fact be inclusive of all Cylons, which may just include Baltar. However, this is likely a metaphor regarding Hera's half-Cylon/half-human nature. In this regard, Baltar represents humanity, being the 'father', and Six represents the Cylons, being the 'mother'. Thus when Six tells Baltar that Hera is 'our' child, she is speaking as a Cylon to a human.
In "Home, Part II", the virtual Six indicates that Baltar's and Six's child will be born in the isolation cage built for the Galactica copy of Sharon Valerii. The reality turns out different: The Caprica version of Valerii, pregnant by Karl Agathon, occupies the cage, and virtual Six indicates that it is in fact Valerii's child that will become Baltar's. This gives some weight to the Baltar-as-Cylon theory since Baltar becoming a father by surrogate circumvents the need for him to do so naturally, although Chief Tyrol's outing as a Final Five Cylon shows that male Cylons can sire a child with human females. However, earlier in the first season, in "33", Six asks Baltar if he wants to procreate with her, and at this point she may mean an actual child of Baltar's. "Home, Part II" occurs much later, and it is possible that the Cylons and Number Six had to alter their plans during this time. Number Six mentions in "Home, Part II" that she doesn't consider Sharon "worthy" of bearing one of "God's new children" (the humanoid Cylons). Perhaps Sharon was not originally planned to be the first mother of a hybrid baby at all, and Number Six was going to have a child with the (necessarily human) Baltar, but had to shift plans when Sharon becomes pregnant first.
With the actual consciousness of the Cylon known as Caprica-Six returned (now with a virtual Gaius Baltar that haunts her), the credibility of the virtual Six, and her connection to some elaborate Cylon plan for procreation with Baltar, is specious at best.
Inside Baltar's Head
Baltar's brain scan in "Home, Part II" confirms that the virtual Six that only Baltar can see is not an actual artificial device in his brain. This leaves a number of possibilities, of which the strongest are:
Possibility #3 is interesting in that, based on Baltar's own research on the Six copy known as Gina Inviere, Baltar's personality and guilt would continue to plague him either in Cylon or human form. But, if Baltar were reconstructed as a Cylon, the virtual Six aids Baltar by being, in effect, the conscience and "guardian angel" she claims to be, keeping his neuroses and guilt over the genocide from driving him completely insane--for now.
The episode "Torn" introduces the Cylon ability known as projection. This ability allows a Cylon to visualize a pleasing environment that also makes it easier to make their way through a basestar's corridors. At this point, Baltar, recalling the many times where he and his virtual Six have enjoyed time at his home in a manner similar to projection, begins to question his own nature.
But Cylons aren't human clones
As Cylons aren't copies of humans, this would suggest either of two possibilities for Baltar: first, that he survives the blast and escapes, or second, that Baltar is a Cylon all along, even on Caprica.
The idea of Baltar being originally a Cylon has problems, however. If Baltar were a Cylon, it would be redundant and unnecessary for Number Six to "choose him" for her mission (unless the Cylons preferred Baltar to remain a "sleeper" throughout his mission to give "plausible deniability" in his mind as well as allow him to do what his personality is likely to do). Furthermore, from a story perspective, the idea of Baltar being a Cylon very much goes against the idea of Baltar as a traitor betraying humanity to the Cylons—as well as the idea of Baltar's relationship with Six being a true human/Cylon pairing. It should be noted, however, that Ron D. Moore's "Gaius Baltar" differs significantly from the "Baltar" of the Original Series. The Baltar of the Original Series is a true turncoat with megalomaniacal tendencies; Gaius Baltar, on the other hand, is not power-hungry but is driven by a strong sense of self, albeit to the exclusion and ignorance of the needs of everyone else.
Baltar is often treated by Six as a human--ultimately the only human who will be allowed to survive by the Cylons. But the human models of Cylon also behave with classically human qualities (not all of them perfect or utopian) and seem to see each other in varying emotions (admiration and contempt are prevalent when Six speaks of the pregnant Caprica Valerii). So, at the least, Baltar is treated with no less respect than any other humanoid Cylon by his virtual Six. If ones assumes that he is indeed human, Six's interaction with him (given the hostilities of the Cylons) borders on admiration. Although Six's emotions can't necessarily be used as a de facto gauge of Baltar's genuine humanity, it does lend to the mystery.
The storyline possibilities do change somewhat if Baltar has always been a Cylon. Baltar has never spoken of his family or other friends (other than President Adar), strongly suggesting Baltar has been a "loner." If Baltar's parentage cannot be confirmed, then the laws of physics (nuclear shock wave damage to human tissue) as well as the laws of procreation (Cylons can't quite procreate as humans do) continue to leave open the possibility that Baltar is model of Cylon, however reduced the odds are now, based on Moore's new information.
Events from the episode "Downloaded"
The episode "Downloaded" contains revelations that reduce the possibility that Baltar is a Cylon. In dialogue with each other, numerous Cylon characters distinctly refer to Baltar as human. Although it is possible that they might keep the information from Baltar, the nature of the Cylon thought collective would seem to make no sense to keep it a secret to each other. In addition, this episode introduces the concept of a Number Six copy with a virtual Baltar in her head. Through Six, Baltar pushes for the Cylons to be more human; for example, letting Samuel Anders go free despite his destruction of a building and many other Humanoid Cylons. If Baltar were a Cylon, the events in the episode would make little sense.
"Torn" renews speculation
The episode "Torn" contains certain revelations about the nature of the Cylons and some possible hints about Baltar's nature. While guiding Baltar through the interior of the basestar, Caprica-Six reveals the Cylon process of "projection"; an ability to alter their perceptions and create a simulated reality of their choosing. Baltar immediately notices how similar that seems to his own visions of Six and begins to question if he is a Cylon. The question still remains, if he possibly is a Cylon, why do the other Cylons think he is a human?
When Baltar questions why he has seen only seven humanoid models, despite the point that twelve humanoid Cylons exist, Caprica-Six is unwilling to answer. Apparently the Cylons have blocked or lost all knowledge of the these so-called Final Five Cylons. With four of these known to the audience, this leaves the possibility that Baltar is the final unknown Cylon.
An additional mystery is the fact that after activating some unknown device in the Temple of Five and getting a glimpse of the Final Five, a Three seems to recognize one of the Final Five and repent her actions. One possibility is her earlier behavior towards Baltar, such as torturing him (Rapture).
Baltar as an "Agent of God"
Baltar's actions when forced by his virtual Six to repent and worship the Cylon version of God leaves several significant questions as to the nature of both the virtual Six and Baltar's nature.
In the episode, "The Hand of God", Baltar makes an educated guess at the specific target to be destroyed on the tylium refinery without knowing any significant data on the site. Baltar only receives encouragement from his virtual Six to trust in her belief. In "Six Degrees of Separation", a stricken and nearly-criminally exposed Baltar repents to the virtual Six just as Lt. Gaeta arrives to confirm his innocence. In the same episode, the virtual Six disappears in anger just as the Shelly Godfrey copy arrives (with a suggestion that the virtual Six knows (or summons) the Godfrey model to arrive. The Godfrey model disappears just as the virtual Six returns as Baltar is repenting.
"Downloaded" strongly suggests that the virtual copies of Caprica Six and Baltar that haunt their opposite interests seem to be psychological remnants of the pair's intensive emotional connection. But what if there is more to this than psychology? Episode events surrounding the Sacred Scrolls and Laura Roslin's quest for the Tomb of Athena confirm that the Colonials have a spiritual or prophetic element that has guided them to the data that now places them in a true general path to Earth. What forces are driving Baltar beyond his own egotism? What is the nature of the virtual Six and Baltar? Neither Baltar nor Caprica Six know why they appear, and both virtual beings appear to have knowledge beyond that of what the living being they haunt should know. If Baltar is being influenced by the Cylon God (or some cybernetic influence known by neither Cylon or Colonial), there suggests a new thread to the Baltar-as-Cylon speculation that goes beyond the mere creation of a Baltar model. However, in the episode's podcast, Ron Moore speaks of the virtual Baltar as simply a hallucination, while in other interviews and podcasts, Moore consistently states that the origin of the virtual Six is supposed to be deliberately vague.
Baltar as Cylon Christ
The Cylon God is speculated to also have been a Lord of Kobol, "the one whose name cannot be spoken" or "the jealous god" who prompted the battle on Kobol. If so, he is/was a real being on Kobol of similar state to the other lords, and could have a physical incarnation, containing whatever portion of his mind could fit in a humanoid brain, among the Fleet. Baltar could be more than an agent of God, or a Cylon, he could be an (unaware) actual incarnation of the Cylon God in the "Christ" motif which is extremely common in literature. The Season 4 episode title "He That Believeth In Me" is a direct reference to Christ, and in fact Baltar becomes the messianic leader of his own cult during the episode.
On a more obvious, visual level, Baltar, on several occasion is seen to be in the pose of Christ on the cross, for example in the water, in his drug-induced vision in "Taking A Break From All Your Worries" or when he collapses in the grass on Kobol. Additionally, after his return from the Cylons, his hair and beard begin to resemble what most people would typically imagine Jesus's to have been like.
Baltar is smarter than not just other Colonials, but also apparently than the Cylons in some areas, discovering clues to Earth they can't figure out in spite of their computer memories and claimed superior knowledge of the Sacred Scrolls. Baltar's inner Six claims to be an angel sent from God to protect him. At the same time, Caprica Six's equivalent appears in the form of a Baltar. Baltar's inner Six's first mission is to arrange a religious conversion for Baltar.
Baltar is identified as a superior intelligence by the Hybrid which also names him as "the Chosen One."
As noted, the theme of divine incarnation for redemption is a very common one in fiction. Ron Moore has a known penchant for redemption drama, and Baltar as a Christ-figure, redeeming himself and then both humanity and the Cylons potentially, fits with this.
The First Hybrid who says his children believe he is a god, makes a prediction about the final Cylon: "...the fifth is still is in shadow, drawn toward the light, hungering for redemption, that will only come in the howl of terrible suffering." (Razor) This statement, while not concrete, may relate to Baltar. Of the major living characters, he most has begged for redemption, and is most in need of it, and it will indeed be painful for him. While Lee Adama seeks redemption for the Olympic Carrier this has been at best a minor theme in his character. Only Baltar begs for it, and only Baltar has said he would find redemption in learning he was a Cylon.