Clara's frightened pleas are mistranslated into Dalek-style, and only the word "mercy" alerts the Doctor that this is not a true Dalek but a human trapped inside a Dalek casing. The implication is meant to be that Davros incorporated "mercy" into the Daleks' vocabulary from the very start, because the Doctor's rescue of him had made an impression on him even if he had grown up to be a genocidal sociopath. Davros just told him that these Daleks allow him to use their life force to survive because "My Daleks are afflicted with a genetic defect. Respect. Mercy for their father. Design flaws I was unable to eliminate."
Why is the Doctor so willing to use up so much regeneration energy to outgambit Davros? What is Rule #1? The Doctor probably did something clever that only resulted in a tiny bit of regeneration energy going to the Daleks, like Eleven did to fool the Fixed Point in time during "The Impossible Astronaut".
It's also possible that the Doctor had already decided that he would be the last Doctor; he wouldn't care about the loss of Regeneration energy if he never intended to regenerate again.
Colony Sarff spends much of this episode hanging from the wires in Davros's infirmary, including the scenes where Davros attempts to persuade the Doctor to use those same wires to commit genocide on the Daleks. We see later that Sarff is there mainly to restrain the Doctor, making these earlier scenes a bit of Fridge Brilliance for Davros for trying to dissuade the Doctor from his compassion for all life, toward Davros's own pragmatism, while having arranged everything in advance so that even if the Doctor did agree to destroy the Dalek race, there would be no danger at all of that actually happening. Davros would have made his point about the Doctor, and Sarff would have kept the Daleks alive anyway.
All the way back in "Davros", half a lifetime ago for both of them, Davros told the Sixth Doctor that he considered him, in a strange way, the only thing like a friend he had - his intellectual equal, the only person he's able to talk with. Ol' Sixie was not happy. ("We're not friends, Davros.") But it does make you think that when Davros tells the Doctor he's happy he has his people back, and shares a joke with him, he's not lying. Sure, he's a sadistic megalomaniac who is trying to trick him into something, but that doesn't mean he's not telling the truth at that moment. And in a gesture of kindness to a dying enemy, Twelve quietly accepts it this time without argument.
Missy openly admits she stole one of the Doctor's ideas to provide herself and Clara with a means of escape. If you think about it, the Doctor stole one of Missy's ideas here, too ... namely, reanimating the occupants of the local graveyards to unleash them on the living. In this case, it just took a lot less Cyber-upgrading and was a lot more disgusting to witness.
Of course Clara deduced how the Doctor dealt with the invisible assassins. It's exactly the same ploy Clara herself used in "Flatline": mooch the power you need off the bad guys' own attacks.
Due to their different points in time, The Doctor and Davros have different perspectives on The Doctor's actions and emotions through this episode. For The Doctor, there is shame at having abandoned a small child on a battlefield, no matter who they grew up to be; but for Davros, knowing that The Doctor went back for him, he would believe that shame must be at showing mercy to a vulnerable enemy. This ties in with their stated perspectives on compassion during the episode.
The Daleks could be the poster boys for Why Don't You Just Shoot Him?, considering the number of times they've let the Doctor natter on with their guns trained on him, only to have him somehow defeat them. Asylum of the Daleks proposed that they may just admire his hatred of them too much to pull the trigger, and The Time of the Doctor suggests that they're afraid he's got tricks up his sleeve even when it least seems that way (hence their hesitation to fire on an Out of Continues Doctor reaching his end from old age), but this episode may offer an alternative explanation. Daleks need to channel their emotions through their guns to fire, all their rage and hate, and that might make it difficult to shoot the Doctor: they are scared of him. The Doctor's flippant babbling in the face of them could also be a form of Confusion Fu; seeing their worst cultural nightmare face-to-lack-of-face might knock them off balance for a few precious seconds, but acting like a fool will keep them that way longer.
There's a trace of tragic karma about Clara's dilemma, being unable to say what she must to inform the Doctor it's really her inside the Dalek chassis. It's the same dilemma which she'd posed for the late Danny Pink, when they were talking through the connection to the Nethersphere and she kept demanding he say something to convince her that he was real. The only difference is that in this episode, validating her identity saved Clara's life; in "Dark Water", Danny refusing to validate his (which would have provoked her to suicide) is what saved her.
Missy's using the Daleks' energy weapons to charge her vortex manipulator may also explain how she survived being seemingly disintegrated by the Brigadier in "Death in Heaven" (unless she simply was uploaded to the Nethersphere and then escaped it).
The willingness that common Dalek soldiers display to die for the cause - always a bit incongruously-selfless, given how deeply evil their kind otherwise are - makes a lot more sense, now that we know what sort of nightmarish "old age" they're fated to suffer if they don't get killed in battle.
This one is very subtle and is almost a YMMV case depending on how one considers the relationship between Clara and the Doctor. Missy makes a point out of getting Clara to say "I love you" while in the Dalek, which comes out as "EXTERMINATE!" Considering that she is well aware of the bond the Doctor and Clara share (whether platonic or non-platonic is irrelevant in this context), a fact later referenced in "Hell Bent," and that her ploy involves tricking the Doctor into killing Clara, what better way than to have Clara - as a Dalek - come out and say "EXTERMINATE!" - a word the Doctor has been hard-wired to react to with force? If Clara had said "I love you" inside the Dalek, she would have been killed without thought by the Doctor. Instead, Clara takes a third option and gets the Dalek to say "mercy" instead, which prevents this from happening - by expressing her feelings for the Doctor in another way. Recall that in "Death in Heaven," Clara promised Danny she'd never say "I love you" to anyone else (her utterance at Missy's request doesn't count as saying it to anyone). So of course she would have said something else in order to keep her promise to Danny.
The Doctor preference for the Indy Ploy is justified after discovering (in Missy's story about his escape from the android assassins) that he can calculate much faster than a human can — what seems like a last minute ploy to us is actually a long time for him.
The Reveal that the Master had a daughter and the Doctor knew her may also help explain the noticeably increased contempt the John Simm Master incarnation showed towards the Doctor in previous series, to the point of refusing to regenerate and letting himself die rather than give the Doctor the comfort of knowing he wasn't the Last of His Kind; if the Doctor knew the Master's daughter and she lived on Gallifrey at the end of the Last Time War, she would have presumably been among those the Doctor and the Master both thought he'd killed when he destroyed Gallifrey. This may be a factor in why the Tenth Doctor was so reluctant to harm the Master, as he would've been guilt-stricken at the thought of having murdered his oldest friend's child and having to face him after. Missy, the next Master, knew Gallifrey hadn't been destroyed as previously thought, and was more forgiving towards the Doctor.
Granted, that's assuming the Master's child was still alive by the end of the Time War. If that wasn't the case, perhaps the Master'd already hated the War Doctor for not joining the war sooner, in which case Missy's previous attempt to force the Doctor to become a Cyberman-commanding warmonger might've had more than a dash of embittered "See what I mean? This is how you should have done things!" to it. Which isn't that different from what Davros keeps trying to prove his own philosophy correct to the Doctor.
Following that, it also makes sense that Missy is the first Master shown to wear the brooch a previous Doctor had given a previous Master after something involving her/his daughter, and is even willing to mention her daughter, when previous Masters hadn't worn the brooch or mentioned their daughter at all; Missy has proven to be a more sentimental incarnation of the Master in trying to regain the Doctor's friendship, so she is both wearing the brooch to remember her daughter and as a visual reminder to the Doctor of their past together everytime he looks at her.
The reveal in this episode that Daleks are unable to say certain things casts a new light on Rusty. Perhaps when he said, "you are a good Dalek," what he actually meant was, "you are a good person."
Unlikely considering that Clara was forced by the voice encoder to say "Dalek" when she was using her concept of self. Daleks have been shown to be able to use the word "individual" or "person" before, Rusty really meant what he said.
The Doctor telling Missy to run at the end of this story. Partially, it's because he's absolutely furious with her, but also because he knows she's perfectly capable of getting out by herself.
Fridge Horror
Sure, the sewer Daleks rose up and destroyed probably most of the infrastructure on the planet's surface. But the Daleks can fly. It's a safe bet that many if not most of them escaped the overflow, and they still have the Time Lord upgrade, whatever that entails.
The degraded Daleks from the sewers have supposedly killed all the normal Daleks on Skaro. Okay, then what? They have Regeneration Energy. Can they regenerate into younger forms and take over the now-empty travel machines? Are they still sludge, but able to act intelligently, possibly setting loose a Dalek menace that can ooze under doors and through vents at will wherever they choose to conquer?
Doubtful; there's only so much regeneration energy per Dalek to go around.
The Doctor comments that the little spark of regeneration energy he's going to share with Davros may cost him a limb down the line. What will the much larger amount of energy Davros stole from him end up costing the Doctor? Perhaps being unsure of how much regeneration energy the Metacrisis had used up was a reason for Eleven checking on whether he had all his limbs after he regenerated.
Thanks to the events of "The Time of the Doctor", the Doctor has an unknown number of regenerations and may have much more energy to spare than before.
He also said that he might just be shorter somewhere down the line. Since regenerating, she's definitely lost a lot of height.
When Clara is hooked up to the Dalek travel machine, her more benign statements get dubbed into phrases like "I AM A DALEK" and "EXTERMINATE!" One wonders if the travel machines are meant to gaslight any "deviant" Daleks into compliance. If a Dalek starts to question the need for endless war, he'll feel all alone in the world, especially if his questions about how he feels are censored by his source of mobility and protection, leading them to questioning their own sanity and conforming as a coping mechanism. You got to wonder how many "good" Daleks the Doctor has killed because he had no way of knowing about these sentiments.
This episode highlights just how clever and manipulative Davros is. He figured out that his childhood encounter with the Doctor was actually two encounters, and managed to spot the point in the Doctor's timeline when he had abandoned the younger Davros but had not yet gone back to save him after all. Davros made sure to contact the Doctor during that brief, critical gap when he would be feeling most guilty and be most vulnerable to manipulation. Who knows how long ago Davros figured out what happened? How long has he had this strategy in his back pocket, so to speak, waiting for the right moment to take advantage of it?
