#everyone's just looking for a little human/ghost connection up in this asylum tonight
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Ch. 2: “Extremis” Analysis Doctor Who S10.6: 3 Masters & Is the Doctor Hurt Worse than We Think?
More Oddities
There are plenty more oddities in “Extremis” whether it’s the Vault, Missy, the Doctor, the Master, the Veritas, etc.  Because time is short to post a second chapter, you’ll have to excuse the flow of things.  “Extremis” has so much to talk about, and I want to get at least some of this out.
The 2 Liars
Moffat has a sense of humor in the subtext.  I forgot to mention something in my previous chapter that I find really amusing, which supports my hypothesis that this Doctor is real.  In the Oval Office, there are 2 chairs, one on either side of the president’s desk.  Check out the patterns in the backs of the chairs.  They are lyres, most likely a play on liars.  There also happens to be 2 Doctors, 2 crosses, and 2 images when he sends the email, too.  This Doctor is lying about whom he is.  Not only that, his faint inverse reflection shows up on the desk.  He is opposite to how he appears.
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He would have to lie, so as not to give away any plans he has.
BTW, at the end of “Oxygen,” when the Doctor is talking to Bill, we see a stoppered liquor decanter (red arrow) near the window and Beethoven.  It looks empty, but it may not be.  If it’s not, he has strong fears about what has happened, especially with his blindness.  However, emptiness represents loss of hope, which seems very likely.  He is literally running on empty, feeling like he has nothing left to give.  This certainly goes along with taking one’s life, and the suicides in “Extremis,” including the president’s.  The other thing here is the chess set (white arrow).  This is war, which is tied up with potential fears and his loss of hope.
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 The Master from Old
Long before Season 10 started, I said a lot of old cast members had to come back.  I’m not surprised at all that John Simm would come back as the Master.  In fact, I expected it from the subtext, which shows some surprising things.
“The Sound of Drums”
This image below is from “The Sound of Drums,” John Simm’s first episode as the Master.  I’m not counting his previous one, “Utopia,” where he regenerated at the end.  
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Anyway, check out his inverse reflection (yellow arrow).  He and the others are not as they appear.  However, something is even more curious.  Notice the little Roman columns (white arrows) above the fireplace. This ties him to “The Fires of Pompeii” and the 12th Doctor.  It also ties him to the Library because there are 4 columns in each set. Four is associated with the Library, I believe, because the 4th Doctor integrated with Morbius, which, I also believe, comes back to the Eye of Harmony.
We’ve seen how the Master is associated with CAL and the drums in the Library.  However, there’s a much more surprising thing, which I’ll show you in a few minutes.
This image below is another example of something not being the way it looks in this episode.  In fact, the 10th Doctor, Martha, and Captain Jack Harkness are in many skewed scenes.  This image with Jack comes from Martha’s apartment.  Here, Jack is associated with a sea turtle (yellow arrow), a 12th Doctor symbol.  He’s also associated with the 3 legs, the triskelion (white arrow), which is a symbol of the Isle of Man.  It also has more connections tied to the 12th Doctor, which I’ll explain in a few minutes. Additionally, the red arrow points to a statue of a dancer.  The surprising thing is whom these items are associated with, besides the 12th Doctor.
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In “The Impossible Astronaut,” Amy has the same symbols associated with her on her refrigerator, except the dancer.  For that, Amy has a print of a dancer on her wall in another scene.  She also dances in “Asylum of the Daleks” when she is under the illusion that the Daleks are people dancing.
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I won’t be surprised if Amy and Jack show up.  I am expecting Amy for multiple reasons.  For similar reasons, I believe we will see other characters, like River, Clara, Rose, and Donna.  I’m expecting Susan to make an appearance.  This would be great if it happens, don’t you think?
“The End of Time” Parts 1 & 2
In “The End of Time” parts 1 & 2, the Master turns everyone into himself, except the 10th Doctor, Donna, and her grandfather Wilfred.  In these last 2 episodes of the 10th Doctor, the Master has more ties to the 12th Doctor.
Most of the scenes play out in the Library metaphor.
But there are other similarities.  For example, in this image below, one version of the Master is associated with the number 3, symbolizing The Ghost.  Other versions of the Master come out of other doors in this apartment building, but those numbers are dull, or the numbers have fallen off, leaving a faint print of the former number.  This number stands out.
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 Here’s a close up of another version of the Master.  There were several, versions of him, like the one below, who are associated with Santa. In “Last Christmas,” Santa is associated with the 12th Doctor.  In fact, Santa represents the Doctor’s psyche, which suggests the Master is part of the Doctor’s Vault metaphor, his mind.
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Here are several clones in the image below.  By turning every human into himself, he is like the Empty Child going around spreading the plague of physical changes from a template, like little Jamie did.  We’ve seen this in the subtext with the 12th Doctor, too.
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Here’s the really shocking part.  Well, it’s not so shocking since “The Deadly Assassin” is so heavily referenced, but still… The Master is associated with the horse and rider from “The Beast Below.”  He is an architect of what is going on with the 12th Doctor. We know Missy is an architect, too, because she was using Clara to manipulate the Doctor.  However, this image below, along with the other things I mentioned above, suggests the Master, himself, has something to do with the 12th Doctor. Notice, too, that the horse is behind bars, like the Master.
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Here’s the President of the United States below, who now is another version of the Master.  In “Extremis,” we see the 12th Doctor at the president’s desk.  In many ways, the 12th Doctor is mirroring the Master.  This begs the question of whether the Master, Valeyard, or someone has usurped the Doctor or his body.  I am sure something has been usurped because that theme keeps coming up in the subtext of several episodes.  For one, we saw it with Shakespeare’s As You Like It.  I’ll show you more in a few minutes.
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In yet another example of mirroring, the Master was always wanting to eat a lot because he was running an energy deficit.  The 12th Doctor is mirroring the Master by also eating a lot.
BTW, Bill in “The Pilot” says something that connects to the Master.  She is trying to talk the Doctor out of a mind wipe and says
BILL: Okay, let me remember just for a week. Just a week. Okay, well, just for tonight. Just one night. Come on, let me have some good dreams for once. Okay. Do what you've got to do. But imagine, just imagine how it would feel if someone did this to you.
I found this to be really interesting because in “The End of Time” episodes, people were having bad dreams, signaling the return of the Master.  I took Bill’s statement to be a signal that the Master is returning.
In “The Pilot,” they also travel to a planet that reminds me of the Ood’s planet, which is where “The End of Time” started.
The Sicilian Legend of the Triskelion & Medusa
While the triskelion that we saw with Jack and Amy is different from the image below, there is an important connection in the subtext of multiple episodes to an associated legend. This image from thatsarte.com is a symbol of Sicily and of the story of Colapesce, which has a connection to the 12th Doctor.  Not only does it contain the 3 legs, but also it has the head of Medusa.
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A Sicilian boy named Nicola, nicknamed Cola, loved the sea and spent his days swimming and diving.  Because of this, everyone called him “Colapesce,” where pesce means fish.  He lived in Messina, a beautiful city in the east coast of Sicily, with his mother.  She didn’t like Cola’s habits and told him that he would change into a fish sooner or later. 
Because of the enormous amount of time in the water, his body started changing. He became more like a fish, diving at greater depths without any effort and staying underwater for many hours.
The boy was very popular because he helped the sailors to avoid the dangers at sea and he always came back to shore with a great story to tell about the treasures lying on the bottom of the sea.
When King Frederick II learnt about Colapesce’s extraordinary skills, he sailed to Messina to meet him off the coast. The sovereign threw overboard a golden goblet and asked the kid to dive and bring it back. Colapesce did not waste any time: he plunged, came back promptly with the precious goblet and narrated the wonderful submarine landscape he had just admired.
Impressed, the King asked the crew to sail where the water was much deeper and threw overboard his crown. It took Colapesce two days and two nights to find the crown and when he came back he told Frederick II that he’d discovered that the island of Sicily rested on three columns: the first was intact, the second was chipped and the third was about to break.
Frederick II was now even more intrigued and decided to throw into the water one of his rings. This time Colapesce hesitated because he sensed that he would not come back. At last he decided to go and said: “Give me a handful of lentils. If you see them surface, you’ll know I am not coming back”. A few days went by without any news, then the King saw some lentils and his ring return to the surface. That’s how he learned that Colapesce had decided to stay under the sea and take on his shoulders the broken column.
Ever since, whenever an earthquake shakes the island the Sicilians know that it’s the poor Colapesce being tired and moving the broken column on his other shoulder.
By the way, this ending adds support to my hypothesis that the Doctor will stay in the Library metaphor, which most likely is Gallifrey, with River and Clara helping to be the protector of Gallifrey.  He really doesn’t have to regenerate.  Just print a copy of the original.  We’ve seen how Gallifrey keep biodata on each Time Lord.
Theme: People Turning Human
One theme running through DW is that people who have turned human, like the 10th Doctor in “Human Nature” and “The Family of Blood,” end up doing cruel things that they normally wouldn’t do as a Time Lord.  So this legend very much speaks to this theme of spending too much time on Earth and turning human.
In another example out of so many, we see this in “Planet of the Ood.”  Halpen, the man in charge of Ood Operations, was an Ood in the subtext who had become human. Ood Sigma turned him back into an Ood, his original form.
The Connection to Medusa
The symbol above also contains the head of Medusa, who has an important place in DW. We examined how the Daleks stole the Doctor and The Ghost before and took him to the Medusa Cascade.  The Doctor has ended up there twice that we know of like he said in “The Stolen Earth” and “Journey’s End.”
Also, there is a very important connection to what is going on in “Vincent and the Doctor.”  In the image below, Vincent Van Gogh (blue arrow) is standing in front of the statue of Perseus with the head of the slain Medusa (red arrow).  Vincent is Perseus.    The monster he defeated represents the monster Medusa, who could turn people to stone.
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Of course, Medusa’s head is the symbolism of a beheading, which we’ve been seeing over and over again.  Right from the 1st episode of the 12th Doctor, “Deep Breath,” beheading was a theme.  The hot air balloon the half-faced man had was the SS Marie Antoinette, referring to the beheaded French queen.
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However, Vincent’s Medusa is represented by the blind, invisible Krafayis, who, because he was afraid, lashed out and killed people.  The Krafayis is a metaphor for the Doctor along with Vincent, and both represent the 12th Doctor.
The episode shows Amy, who in the subtext is the Doctor’s Mother of God consciousness, uniting with Vincent, like the landlord’s mother united with the landlord. The idea here is that the plague of deaths stopped in both cases.  This is another reason why I believe Amy needs to show up.  Lucy in TRODM is also a mirror of Amy, which is more subtext showing this will happen.
All of this symbolism and more going back to something in a 9th Doctor episode is why I have believed for many years that the 12th Doctor had to be blind physically at some point.  Then, when “The Return of Doctor Mysterio” showed us the red-tipped, white cane in the subtext, a symbol of physical blindness, I was pretty sure DW was going to make the Doctor physically blind.  Still, I couldn’t rule out metaphorical blindness.
How does this relate to what we are seeing in Season 10?  The subtext suggests that the blind Doctor, being the blind Krafayis, is afraid and will lash out, killing innocent people.  So the seemingly empty liquor bottle that we saw above, would seem, in this case, to also symbolize the Doctor’s strong fears.
He’s personally under assault in so many ways that we’ve never seen before in DW.
The usurpation I spoke of, most likely, is related to the blind Krafayis Doctor mirror looking like the Doctor.  The Krafayis is a ghost and is related to the Sun stage of the Great Work and the plague.
In fact, “The Time of the Doctor,” the last 11th Doctor episode, gives us more information. The Doctor mirrors Tasha Lem in this scene, where both show the same significant painting behind them.  Sadly, I haven’t gotten this chapter posted, either, on Religious metaphors.  So this is a small part of that chapter.
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Here’s a better image below, showing more of the painting.  It illustrates a biblical passage.  There’s a Dalek in front of The Expulsion of Heliodorus from the Temple, a popular biblical topic among several master painters.  Francesco Solimena painted this version, circa 1725.
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This scene illustrates the biblical episode from 2 Maccabees (3:21-28), which is about God punishing the wicked and restoring the Temple to his people. (Catholics and the Eastern Orthodox regard 2 Maccabees as canonical.  However, Jews and Protestants do not.) 
The king of Syria sent Heliodorus to seize the treasury in the Temple in Jerusalem, so the priests prayed to God for help.  God sent 3 spirits in human form.  The main spirit was a horseman, which The Revised Standard Version, Catholic Edition, called “the Sovereign of spirits and of all authority.”  He and the 2 younger men easily overpowered the terrified Heliodorus and his men, who all came to recognize the sovereign power of God. http://biblia.com/bible/rsvce/2Mac3.21-28
Heliodorus is a significant name in that it means “Gift of the Sun.”
The Sun has to die alchemically, which we’ve examined before, to stop the plague and move to the next stage of the Great Work.  This painting confirms the Sun as the usurper.  That’s not surprising, but who all is controlling the Doctor?  In the case of the Empty Child, the Chula nanogenes were controlling the plague.
The Woman in the Shop
In the Library episodes, the 10th Doctor and Donna made a big deal of the Library’s gift shop.  In fact, there’s a spot in an episode where River’s reflection shows up on the shop’s window.
“The woman in the shop” is a metaphor for Missy.  Because of the association, I have been wondering for a long time about this.  This may suggest that River is related to Missy.
What is clear from “Silence in the Library” and “The Forest of the Dead” is that River has a hidden face. One of River’s hidden faces is Amy, another is the Doctor, himself. Does she have another?
The Vault & 3 Masters
The Vault is not as it seems.  In fact, if you look closely at the image below, there’s an inverse reflection (yellow arrow) of the Vault in the water.  Therefore, things are opposite with how they appear with the Vault.
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Several chapters back, I mistakenly said there were 44 Circles in the Squares on the front of the Vault because none of the images actually showed the top row of the Vault. There are 46 Circles in the Squares. That’s worth three 12th Doctors and one 10th Doctor.  However, it also looks like there are 54 Circles in the Squares on the side of the Vault.  That’s a lot of Doctors.
All of these Circles in the Squares represent alchemical integrations, like what we saw with the Doctor and Clara when they went into the Vault of the Bank of Karabraxos.  The Circles in the Squares also may indicate power. Whatever is in there, is very powerful.
3 Brainstems
At the beginning of “Extremis,” Rafando explains how the weird setup of the technology in the image above works.
RAFANDO: This technology is precisely calibrated. As you can see, it will stop both hearts, all three brain stems, and deliver a cellular shock wave that will permanently disable regenerative ability.
What I didn’t expect was 3 brainstems.  According to Wikipedia, “The brainstem (or brain stem) is the posterior part of the brain, adjoining and structurally continuous with the spinal cord. In the human brain the brainstem includes the midbrain, the pons, and the medulla oblongata. Sometimes the diencephalon, the caudal part of the forebrain, is included.”
The image below from Wikipedia shows the 3 parts of the human brainstem.  Of course, Time Lords could be different.  
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However, in “The Magician’s Apprentice,” Missy made a comment about brainstems.
MISSY [on monitor]: Okay, cutting to the chase. Not dead, back, big surprise, never mind. I'm in a lovely little square in one of your, oh, I don't know, hot countries. There's a light breeze coming from the east, this coffee is a buzz-monster in my brain, and I'm going to need eight snipers.
KATE: Eight what?
MISSY [on monitor]: Three for each heart, and two for my brain stem. You'll have to switch me off fast, before I can regenerate. How fast can you get here? Ooo, I'll need to arrange you a flight corridor.
She, of course, could be lying about having only one.  However, she may not have been at the time because there’s another possibility we’ll examine shortly.  Also, no one actually said Missy had 3 brainstems in “Extremis,” just that the equipment could handle 3.  It does leave me wondering because this is new information.
However, let’s assume that she has 3 brainstems.  For a human, that would suggest that she has 3 brains and 3 heads.  If most everything we are watching is an illusion, then it’s possible. 
In “Vincent and the Doctor,” the 11th Doctor talked about his godmother with two heads and bad breath.  It’s come up in the text before that Time Lords could end up with multiple heads.
3 Masters & CAL’s Library
However, I’ll propose something else, using the symbolic aspect of this.  Three is an important number, symbolizing The Ghost.  Interestingly, there are 3 panels on the door that Missy comes out of (red, white, and yellow arrows), so they lend support to the notion that she really does have 3 brainstems, which can also equal 3 integrations or 3 alchemical marriages, just like the Doctor.
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Are Missy and the Master faces of The Ghost?
Back in Chapter 18 of Fairytales and Romance in Doctor Who, we examined how Rassilon places the incessant drumbeat in the Master’s head.  And how CAL in the Library experiences toy drums beating incessantly when she’s having a meltdown.  This makes CAL a mirror of Missy and the Master, as well as the Doctor, whom we also examined as being connected to the symbolic Drum earworm in “Under the Lake” and “Before the Flood.”
For several years, when I have thought of the ghost in the 12th Doctor’s subtext, I have pictured him in the Library, just like CAL.  And the subtext says the Master is there, too, along with Missy.  CAL represents all 3 of them.  CAL is the metaphor of The Ghost.
Therefore, 3 brainstems are not a stretch at all, although the terminology is surprising to me. This is the idea of the Holy Trinity where 3 people are One.  The Holy Trinity is very much being referenced in DW.
The War Doctor & the Master
In Chapter 19 of Fairytales and Romance in Doctor Who, we examined some surprising things about the War Doctor and the Master.
In “The Sound of Drums,” the Master says something surprising about the war:
MASTER: The Time Lords only resurrected me because they knew I'd be the perfect warrior for a Time War. I was there when the Dalek Emperor took control of the Cruciform. I saw it. I ran. I ran so far. Made myself human so they would never find me, because I was so scared. DOCTOR: I know.
This suggests the Master is the War Doctor.
And TRODM supports this. The Master’s wife, Lucy, was in prison for killing him, just like River was in prison for killing the Doctor.  Lucy is in TRODM because she is the Doctor’s alchemical wife = Mother of God consciousness = Amy => River.  The subtext suggests Amy is a Time Lord, living as a human.  Therefore, River represents Amy’s regeneration. Rory is a mirror of the 12th Doctor, so this all makes sense.
In fact, I need to make a post that shows you how Grant and Lucy’s relationship in TRODM mirrors Rory and Amy’s.  I’ll show you in that post how what we think we see about Amy and Rory doesn’t always happen the way we think.
The Master & Missy
Going by all of this, the Master and Missy are faces of the Doctor.  In fact, Missy says something very curious in “Dark Water” when the Doctor is trying to figure out who she is.
DOCTOR: How did you get hold of Time Lord technology?  Who are you?
MISSY: You know who I am. I told you. You felt it. Surely you did.
DOCTOR: Two hearts.
MISSY: And both of them yours.
Both of her hearts are the Doctor’s.  How is that possible?  I don’t believe she is lying.  This supports her being a face of the Doctor.  She also could be an identical twin.
Earlier in the episode when he first meets her, we learn something interesting.
DOCTOR: Who are you?
MISSY: I am Missy.
CLARA: Missy?
MISSY: Mobile Intelligent Systems Interface. I am a multi-function, interactive welcome-droid. Helping you to help me to help you.
After we learn who Missy really is, her droid comment looks like a joke.  It may be.  However, since Rory is a droid, the Doctor and Missy could very well be, too.
As you can see, what and where the Doctor is is very perplexing and intentionally so.  Putting all the pieces together is the fun of all of this.
Here’s another possibility that has plenty of support, which is further supported by the notion of 3 brainstems.  The Master and Missy are all in the Doctor’s head, like Doctor Moon is in CAL’s.  Like with CAL, we see virtual reality versions of the Master, Missy, and the Doctor.  We see something similar to the idea of nesting when Amy and Rory are in the Teselecta version of Amy in “Let’s Kill Hitler.”
The nesting of one being within another is already a fact in DW.  We see it  (possession) with the Scottish young man in “Tooth and Claw,” and we see it again in TRODM when Harmony Shoal takes over a body. 
In fact, much more is going on with this type of thing.  Not only does Amy have a Russian doll (nested dolls) in her house, but also Amy and Rory show up in the most bizarre set of reflections that I’ve ever seen.  They support the nesting concept.
In the 11th Doctor episode “Asylum of the Daleks,” where we first see Jenna Coleman, Rory has 3 reflections, 3 faces.  The center one is a ghost.  However, the really bizarre thing is where Amy’s hair is (yellow arrow).  This is saying that Amy and Rory are, in one of the faces, nested.  One being inside another.
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And nested beings come up over and over in the subtext and the text, just like CAL in the Library. It happens when there is an integration, when people are absorbed into the system, like how CAL uploads them to her hard drive.
I don’t want to belabor the point here.  I actually could write a lot about other bizarre things in this scene, as well as the entire episode, but that’s for another post.
However, nested beings are already canon with CAL, so this could very well be the case of what we are watching with Missy and the Master.  This has already been posited in “The Impossible Planet,” where the Master is a personality inside the Doctor.
Nested beings could be physical, like in CAL’s case, or personalities of an individual, like in the Doctor’s case with the other Doctors.  We sometimes see the Doctors manifest as separate beings in a single episode.
The 3 Masters
Given how the subtext in multiple ways is saying that the Doctor, Missy, and the Master are related, it is suggesting that the Master is actually another version of the Doctor.  That was part of Chapter 19 of Fairytales and Romance in Doctor Who.  The subtext suggests that Prisoner Zero is the Master, who would be Doctor Zero. 
Here’s the kicker:
On a 24-hour clock, midnight is both 0:00 and 24:00, so the 12th Doctor is automatically ambiguous.  And we’ve already examined how the 10th Doctor at times was playing the 12th and 24th Doctors, which is also shown, for example, by the episode titled “Midnight.”
Therefore, this all suggests that the Doctor is another versions of the Master and Missy. 
How’s that for mistaken identity, if true?
And this goes along with the Doctor fighting himself.
This is why I said in a previous chapter that I wouldn’t be surprised if a face of the Doctor was in the Vault.  After all, the Vault metaphor represents the Doctor’s mind, and all the Doctor’s are within it.
It could be any of his faces, including people like River or Clara, who have integrated with him.
Or will DW give us someone from the past who played a previous version of the Master? 
Regardless, I am convinced from the 3-brainstem statement that there will be 3 Masters.  Will one have the 12th Doctor’s face?
The Ghost & the Triad: Achieving Unity
The Ghost is a part of a triad, a trinity, which links into the Trinity (we’ll examine that in a few minutes).  This triad shows up in “Time Heist.”  The Bank of Karabraxos is an interesting name because it has early Christian ties to the Gnostics with the concept of Abraxas. 
Carl Jung in 1916 wrote about the concept of Abraxas in The Seven Sermons to the Dead Septem Sermones ad Mortuos (Translation by H. G. Baynes)
God and devil are distinguished by the qualities fullness and emptiness, generation and destruction. Effectiveness is common to both. Effectiveness joineth them. Effectiveness, therefore, standeth above both; is a god above god, since in its effect it uniteth fullness and emptiness.
This is a god whom ye knew not, for mankind forgot it. We name it by its name Abraxas. It is more indefinite still than god and devil.
That god may be distinguished from it, we name god Helios or Sun. Abraxas is effect. Nothing standeth opposed to it but the ineffective; hence its effective nature freely unfoldeth itself. The ineffective is not, therefore resisteth not. Abraxas standeth above the sun and above the devil. It is improbable probability, unreal reality. Had the pleroma a being, Abraxas would be its manifestation. It is the effective itself, not any particular effect, but effect in general.
I prefer to explain this visually with the taijitu, which some people refer to as the yin-yang circle, shown below.  It contains more parts than it might seem. Not only are there 2 large light and dark areas, along with 2 small circles of opposite colors, there is the black outline of the circle that contains everything.
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The concepts here mirror what Carl Jung is saying, although the taijitu goes beyond what he is saying above.
When Jung speaks of God and the devil, he is speaking of duality, along with the qualities of opposites suggested by fullness and emptiness, generation and destruction.  Interestingly, he names god Helios or Sun in opposition to the devil.  Abraxas stands above them both, as both are joined together by effectiveness.
The Sun relates to the Doctor being the Sun metaphor.  However, Abraxas stands above him.  This all relates back on a certain level to the Doctor being at the 3rd stage of the Great Work, when he needs to be at the 4th stage.  Right now, he is caught in a duality within himself.
This concept of duality matches the light and dark patterns of the Doctor’s calling card, as well as many other patterns we’ve seen. 
On the taijitu, the large light (yang) and dark (yin) areas represent duality (male/female, light/dark, fullness/emptiness, generation/destruction, etc.).  The small circles within the opposite colors say that there is a little bit of the opposite within.  For example, in light there is a little bit of darkness and vice versa.  As another example, within male, there is a little bit of female and vice versa. 
The small circles could correspond to Carl Jung’s anima and animus, with the unconscious of a man being female and vice versa.  Missy, in “The Witch’s Familiar,” alluded to the meaning in a different way once the Doctor realized Clara was in the Dalek. 
CLARA: Oh, Doctor  
(The Doctor starts to disconnect Clara from the Dalek casing.)
MISSY: In a way, this is why I gave her to you in the first place. To make you see. The friend inside the enemy, the enemy inside the friend.
DOCTOR: I'm sorry, Clara. I'm so sorry!
MISSY: Everyone's a bit of both. Everyone's a hybrid.
Certainly, “the friend inside the enemy, the enemy inside the friend” could be applied to what we are seeing in Season 10.  If, for example, the Doctor does need to die to set things straight, people trying to save him is not a good thing.
Abraxas, in some ways, is akin to the outline of the taijitu, which represents the Chinese word wuji.  This is the monist concept of limitless, infinity, the ultimate beinglessness.  The latter can be a difficult concept for Westerners.  It is the concept of Dao (a.k.a. Tao) from which duality springs. In Daoist philosophy, wuji refers to returning to one’s original nature, which is exactly what the Doctor has been doing through the Great Work.  The Ghost still needs to achieve unity and unite with the Mother of God consciousness.
Interestingly, wu means nothing, nothingness, void.  If we combine the ideas of wuji and Abraxas, we get an additional possible meaning of what the Doctor is saying about the void in the opening of “Oxygen.”
DOCTOR [OC]: Space, the final frontier. Final because it wants to kill us. Sometimes we forget that, start taking it all for granted. The suits, the ships, the little bubbles of safety, as they protect us from the void. But the void is always waiting.
The Doctor has personified the void here, saying it is always waiting.  Given the concept of Abraxas set it above the Sun, I see this as more foreshadowing saying that the Doctor is not above receiving consequences as long as he remains the Sun.  It suggests that we may see the Doctor take on even more damage.  Or has he already that we don’t know about?
Is the Doctor Hurt Worse than We Think?
Missy and the Master may have a field day with the blind Doctor.  However, is he hurt worse than we think?  It would be just like him to conceal all injuries, unless he requires some type of help, like with Nardole. 
This does come back to Donna in “Turn Left” where alternate-Donna had to sacrifice herself to set the universe right.  Mirroring Donna, the Doctor would have to sacrifice himself, but which one is the original? And which one is the alternate-Doctor. Have we even seen the original one in Season 10?
Anyway, in “Extremis,” Bill followed the trail of blood, shown below, that led from the Vatican projection to the White House projection.  Since this room is part of the projection, we can’t tell how real it is. Someone is bleeding fairly badly because there are a lot of big drops, and they are fairly close together.  The person stopped at the entranceway because there are several drops there.  It’s possible the bleeding was stopped because there are a few small drops at the entranceway, not lots of big ones.
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Where did the blood come from?  Obviously, it’s not from the cut (red arrow) above the Doctor’s eye.  There is no blood on his face.  Did he get wounded somewhere else?
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Bill did find the Doctor, but curiously, there was no blood on the eagle carpet in the Oval Office. It’s possible the Doctor did stop the bleeding before he walked across the carpet.  It’s also possible the blood is from another version of him or someone else.
At a minimum, we have subtext proof that emotionally he is hurting a lot worse than it looks.  This doesn’t bode well because the Doctor becomes the most dangerous when he loses hope.  He’ll be the Krafayis lashing out, which is similar to how he was in “Hell Bent.”
On top of emotional wounds, the blood could be metaphorical, which, given the virtual reality, would also make sense.  It could be that the Doctor is hurt physically worse than we think.  He may not be bleeding, but instead dying slowly, which actually makes a lot of sense. 
There are more things in space that can kill besides lack of oxygen.  Radiation bombardment, for example, is a huge problem.  While we’ve seen that he can handle X-rays, the 10th Doctor took on a lethal dose of another type of radiation.
In “Extremis,” what about that reading device he used?  (This is another reason why I think this Doctor is real.)  What payment will it exact if he is real?
The Real Pope Benedict IX
Pope Benedict IX in DW has had a gender change.  The real Pope was a very controversial figure.  Coming from a powerful family, he gained the papacy with few qualifications at the age of 20 in his 1st of 3 elections.  According to Wikipedia,
He is the only man to have been Pope on more than one occasion and the only man ever to have sold the papacy.
His life was incredibly scandalous, and factional strife continued.  The anti-papal historian Ferdinand Gregorovius wrote that in Benedict, "It seemed as if a demon from hell, in the disguise of a priest, occupied the chair of Peter and profaned the sacred mysteries of religion by his insolent courses." The Catholic Encyclopedia calls him "a disgrace to the Chair of Peter."  He was the first pope rumoured to have been primarily homosexual.  Pope Victor III, in his third book of Dialogues, referred to "his rapes, murders and other unspeakable acts of violence and sodomy. His life as a pope was so vile, so foul, so execrable, that I shudder to think of it."
The Cage & Vault Are Mirrors
The Veritas’ cage and the Vault are mirroring each other in certain ways.  The Vault supposedly contains Missy, and the cage contains the Veritas.  Both are under lock and key, so to speak. 
The Haereticum, where the cage is, has been home of the Veritas for over a thousand years.  In comparison, the Doctor is supposed to guard Missy’s body for at least a thousand years.
Missy is in the Vault, while the Doctor is in the cage.  He is strapped in at one point.
The priest had a bunch of food in the cage, while the Doctor took a lot of Mexican into the Vault.
It is very interesting that we’ve been examining the Great Work and seeing the Doctor move from prisoner toward the truth of what’s happened, and now we have a major plot point that translates as “The Truth.”
Interesting Symbols on the Veritas’ Cover
Why does the Veritas have a Latin title when the rest of the book is in an obscure language?  We can certainly make up a reason, but the point really is that it’s odd.  It suggests right away that something might be wrong.
The Veritas’ cover, shown below, is a curiosity for 2 other reasons.  First, there are leaves or perhaps, as my daughter pointed out, stitches on the cover. Second, the red arrow points to a fleur-de-lis.  Both stiches and fleur-de-lis bring in a bunch of subtext.
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Stitches on the Cover
I love the stiches idea because those, such as the ones on the cover, are reminiscent of Mary Shelley’s Frankenstein.  The novel very easily has a place in DW, especially when talking about the resurrected Morbius from “The Brain of Morbius.”  Or even the scar-faced people in TRODM. 
Closer to home, the Doctor keeps talking about putting Nardole’s head back on.  This suggests that the Doctor is taking on a role in a way that is similar to Victor Frankenstein, the young scientist who performs an experiment and creates a creature, which most find grotesque. While Nardole isn’t the grotesque one, as far as we see, it’s the symbolism that’s important.  In another example, the Doctor in THORS was pretending to be the surgeon, who, most likely, was supposed to be Solon, the Victor Frankenstein mirror, from “The Brain of Morbius.”  Then, in another example, the half-faced man, a dark mirror of the Doctor, from “Deep Breath” was also going around taking body parts. It’s a theme.
However, it’s the grotesque Monks, who also are performing experiments.  Yet we see that there is more to them than it seems.
The stiches, then, may very well be a metaphor for elaborate experiments, and it also may refer to real body parts.
Fleur-de-lis & Nardole
The fleur-de-lis is a well-known symbol of not only France, but also of heraldry, suggesting royalty. The most interesting part is that Nardole in THORS, as shown below, is associated with fleur-de-lis.  Therefore, Nardole is associated with the Veritas.  We know Nardole is a mirror of the Doctor, who is of a royal bloodline, if we go by Merlin’s pedigree, and the Prydonian Chapter is a very high-ranking class.  Also, we know Nardole is a proxy in “Extremis” for River, as he reads her words to the Doctor.  By the associations, the fleur-de-lis could represent them all.
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Fleur-de-lis & the Trinity
Not only does the fleur-de-lis suggest royalty, it is found in Christian art until about 1300.  After that, according to Wikipedia, it takes on a Marian symbolism in reference to Mary and the Trinity.  The Fleur-de-lis is used to mark the bloodline. 
Interestingly, the Doctor, near the portrait of the pope, is associated with 2 different statues of Mary. One of them is shown below (white arrow).  I really have little doubt this goes along with the Fleur-de-lis and the Trinity.  It is said that one cannot achieve the Holy Trinity without the Mother of God because she bore the Son, so this is another reason why this is signaling that this Doctor is real.
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However, it could also mean a couple of other things.  Several chapters ago, because of the gender change, I posed the question of whether The Ghost was part of the Father, Son, and the Holy Ghost or it could be Mother, Daughter, and the Holy Ghost.  This particular face of the Doctor would seem to be the Mother part of the Trinity, at least that’s my hypothesis.  That would go along with Jackson Lake, looking for his son, except with a gender change probably for both.
The other question I posed was about how to classify in Jungian terms the Doctor with a gender change – being female inside and male outside.  Would he be the Mother of God consciousness from the Great Work or the male equivalent of the Christ or Buddha Consciousness?  I said I’d stick with him being the Christ or Buddha Consciousness until I saw proof that this should change.  This may be the proof.  It would mean that instead of looking for his Mother of God Consciousness, he would be looking for the male counterpart.  That’s at least another hypothesis, although I don’t weight this highly without more information.  I’m still evaluating what the gender change means.
One thing seems very likely. The fleur-de-lis on the cover of the Veritas refers to the Doctor and his bloodline. It’s highly likely because the one big obstacle to any invasion of Earth would be the Doctor. 
Why CERN?
CERN seems like a strange place to send the Veritas, at least to me.  CERN does research into various things, like creating particles, plasma, and mini black holes. The detection of mini black holes could indicate parallel universes in extra dimensions.  Certainly, particle physics has a lot to do with DW and time travel.  But the importance of the reference pertaining to the actual function of CERN doesn’t seem important to me.  However,…
The answer is probably that the novel Angels & Demons, by Dan Brown, involves antimatter created at the LHC to be used in a weapon against the Vatican.  Dan Brown also wrote The Da Vinci Code.
However, in “Extremis,” being things are backwards, a weapon of mass destruction is sent from the Vatican to CERN.  Where would CERN employees get their hands on explosives like those in the image below?
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Explosives like these are a metaphor for the 7th Doctor’s companion, Ace.  I also believe she might show up.  In fact, this very much reminds me of “The Curse of Fenric.”
ACE: Oh, thanks. I don't know why he used a chemical grenade. If I was him, I've have stuck a few sticks of explosives under the table.
(They look under the table and sure enough - there are the sticks of dynamite and a dangling detonator pin. The Doctor grabs Ace's arm and they run out of building 48, throwing themselves over some sandbags just as the whole building goes KaBOOM!)
This is also a metaphor for Fenric and the curse that we saw was part of Clara and the Doctor’s relationship.  We examined that in Chapter 16 of Fairytales and Romance in Doctor Who.
Crime Scene Images Not Right
When the Cardinal and Pope (the actor was the Italian father in “Turn Left”) are talking about the suicides, images flash by.  Some of them show us there is something wrong.  Here’s an image of the Italian police, which I would expect.
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However, there are 2 images out of about 11 that don’t make sense interspersed in the Italian images. One of these is below.  The police tape is in English.  Later, we also see another image of a gun in an evidence bag that is also in English.  We know that something isn’t right here, and it says that we can’t trust what we see.
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The Doctor’s Desk
Oddly, the Doctor’s desk got turned.  We can see the inverse reflection of the light on the TARDIS, so things aren’t as they seem.  Interestingly, we haven’t really seen River’s and Susan’s photos since “The Pilot.”  We don’t even get hints of them here.
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I’m wondering if that’s because River and the Doctor are now integrated.  Back in “Smile,” there was a reference to “The Wedding of River Song.” Therefore, following the conventions of integrations, River’s image should now be in a Circle in the Square type of frame, not the square-ish frame that we saw.
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