This season of Doctor Who has been pretty tightly structured around a few big themes, and all of them were tied up in the season finale. A lot of them, not surprisingly, had to do with Clara Oswald — and we finally found out why she was chosen as the Doctor's companion. Spoilers!

So all through this season, Missy (whom I'll just call the Mistress from here on out) has been observing Clara's progress from her hideaway in the Nethersphere, and it was hinted in the season opener that Missy pushed the Doctor and Clara together, back in "The Bells of St. John." (When the Mistress gave Clara the Doctor's phone number as a "tech support" option.)

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But why did the Mistress want Clara to be the Doctor's companion? Turns out it's not because of any particular plot device or "Impossible Girl" stuff — but rather, a character trait. Clara is a "control freak," who has spent the past year trying to get a grip on the Doctor, to the point of questioning his morality and even impersonating him.

The Mistress wanted the Doctor and Clara to be together, because she wanted to engineer a moment like the one that happens at the end of "Death in Heaven" — where Clara is so filled with rage at the Mistress, she's willing to commit murder. And the only way for the Doctor to save Clara from becoming a murderer is to do it himself.

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It's basically the classic "You're just like me" thing that villains are always spouting at heroes in pulp fiction — in fact, this is sort of a cover version of Alan Moore and Brian Bolland's "The Killing Joke," among other things. The Mistress has observed all the people who die for the Doctor (because he's an officer, as Danny put it a while back) and she's decided that the Doctor's willingness to overlook acceptable casualties means he's really no different than his arch-nemesis.

So the Mistress aims to use Clara to goad the Doctor into killing her, thus proving they're the same — and in the end, Clara winds up faulting the Doctor not for his ruthlessness, but for being insufficiently ruthless. If the Doctor has ever let the Master live in the past, then all Missy's latest crimes are on his hands.

The Doctor is all set to kill the Mistress to save Clara's "soul." The Mistress asks the Doctor to "say something nice" — the same thing she's said to her victims before killing them — and the Doctor says, "You win." "I know," she responds. (Thus proving that this is what Missy wanted, all along.)

But the Doctor is spared from having to kill the Mistress and get his hands dirty, by the last-minute intervention of the Brigadier, who's become a self-aware independent Cyberman, like Danny.

(And now I want a spinoff show about the adventures of the Cyber-Brigadier, flying around sorting out people's problems.)

So neither Clara nor the Doctor is forced to make the ultimate choice and commit murder — and I guess Missy's plan for Clara is thwarted due to good old Alistair Gordon Lethbridge-Stewart. But before we get to that point, the Doctor and Clara are each faced with another impossible choice: the Doctor is offered power, while Clara is asked to erase her lover.

Clara as both critic and imitator of the Doctor's ruthlessness

We've seen Clara, over the course of the season, go from calling out the Doctor's callousness to trying to emulate it — to be as good a liar as the Last of the Time Lords. And this episode randomly begins with another sequence where Clara pretends to be the Doctor — to talk some Cybermen out of killing her on sight.

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(Clara pretending to be a female regeneration of the Doctor is cute, coming on the heels of the genderswapped Master, and the altered opening credits are nice touch. Also, apparently the Doctor has told Clara about his grandchildren, plural, as well as Jenny, his "daughter.")

But then Clara gets a couple of tests of just how ruthless she can be — the first is when Danny Pink, who's now a Cyberman but still has his human emotions, begs her to help turn his emotions off. This is pretty similar to what happened to that "nice" Dalek in "Inside The Dalek" — the Dalek's memory-inhibitor was damaged, causing it to have memories and emotions that would have been supressed, until Clara and the Doctor repaired it.

Clara wants to help Danny switch his inhibitor on, partly because she can't bear to see him suffer — but mostly out of guilt, it seems like. She feels bad that she wasn't honest with him, and that her attempt to come clean wound up getting him run over by a lorry. (Was the Mistress driving that lorry? Seems likely.) So Clara snaps at the Doctor that he should either help her lobotomize her dead boyfriend, or leave her alone.

Of course, the Doctor does wind up giving Clara the sonic screwdriver, so she can finish deactivating Danny's emotions — but only so Danny can tell the Doctor the next stage of Missy's plan.

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Missy's Cyber-zombies have flown up into the sky, all over the world, and exploded into black clouds of "Cyber-pollen" (don't ask), which has rained down onto the world's graveyards and assorted funeral parlors, reanimating the dead of humanity and turning them all into more Cyber-zombies. But the clouds are still there, and Danny reveals that the clouds are going to rain down more Cyber-pollen and kill all living humans, turning them into more Cyber-zombies.

The only way to stop the clouds from killing all of humanity is for the Doctor to accept Missy's "gift."

The Doctor as general who hates soldiers

One of the two big thematic notes that gets resolved in this episode, with a pretty emphatic resolution, is the Doctor's hatred of soldiers — and the idea that the Doctor is an officer, who gives orders to the soldiers he despises.

The episode spends a lot of time presenting the Doctor with the temptation of authority, something he's never had much time for before. First UNIT sedates him and handcuffs him, before forcing him to serve as the President of Earth aboard a superplane that stays in the air about five minutes longer than I was expecting. And then the Mistress gives the Doctor her "gift" — control over the entire army of Cyber-zombies, so the Doctor can finally have the means to fix all the wrongs in the world.

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The Doctor is definitely not averse to using people and taking advantage of others' sacrifices (as he proves by turning on Danny Pink's inhibitor so he can learn the final purpose of those clouds). But he doesn't know what to do with power or an army — he spends his entire time as Earth President insulting one of his subordinates, whom he dubs "Man Scout" in the latest in a long line of insulting nicknames for soldiers and ex-soldiers. (Others include "P.E." for Danny Pink, and good old "Col. Runaway.")

And when the Doctor is presented with a Cyber-army, it's basically a huge trap. Missy is telling the Doctor that the only way to prevent the Cyber-clouds from killing everyone on Earth is to take command of the existing Cyber-zombie horde and go off and "conquer the universe." Plus the Doctor is presumably a bit tempted by the idea of having a way to free all the people in the Dalek slave camps, and to make the Raxicoricofallaptorians stop farting, and so on.

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"Armies are for people who think they're right. And nobody thinks they're righter than you," says Missy.

Notably, the Doctor doesn't waste any time in this episode mourning for Man Scout — or for poor Osgood, who gets so many brilliant moments before being killed because Missy's guards are asleep at their posts. Or for Kate Stewart, when he thinks she's dead. Because, as the Doctor says in "Mummy on the Orient Express," people with a gun to their heads can't mourn. But also, acceptable losses.

What saves the Doctor from being forced to become a power-mad leader of the Cyber-army? The fact that he was wrong about Danny Pink.

Danny's sacrifice

The Doctor believes that as soon as Danny Pink's inhibitor is switched on, Danny will become just another Cyberman, and will probably kill Clara Oswald. But when Missy orders all the Cybermen to do a silly "safety briefing" routine, Danny is the only one who doesn't obey — he's still got his independent judgment, because of his love for Clara. Love, as the Doctor observes, isn't an emotion — it's a promise.

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(Either that, or the Doctor cheated, and never fully disabled Danny's inhibitor. Take your pick, I guess.)

Because Danny resisted Cyber-control, even with his inhibitor on, the Doctor is able to make a lovely speech about how he's not a good man, or a bad man, or a president, or an officer — he's just an idiot with a box. The Doctor thanks the Mistress for helping to clarify that for him, because sometimes he loses sight of who he really is.

And then the Doctor tosses the control bracelet for the Cyber-army to Danny, who gives his own lovely speech about honoring soldiers and their sacrifices. (Danny basically says the promise a soldier makes to civilians is "You will sleep safe tonight.") And then Danny and all the other Cyber-zombies fly up and burn themselves up, destroying the Mistress' clouds, without the need for the Doctor to become the general of the Cyber-army after all.

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What's ironic, of course, is that Danny's final act proves his point. The Doctor is able to absolve himself and say that he's not a hero or an officer — and thus "keep those hands clean." Because the Doctor knows that when he tosses that bracelet to Danny, Danny will take care of it for him. The Doctor doesn't need to give an order, he already knows what Danny will do.

Or as the Doctor puts it to Missy, he doesn't need an army, because he's got them — meaning both Clara and Danny, but by extension all the other people who've done the Doctor's work for him over the years.

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Meanwhile, Danny finds his own redemption through self-sacrifice — first, by blowing himself up along with the whole Cyber-army, and then, by giving his single return ticket from the afterlife to the Afghan boy he killed when he was a soldier. Instead of returning from the dead himself, Danny saves the boy whose death had haunted him. "I had promises to keep," he tells Clara.

As for the Doctor, he may have learned something about respect for soldiers from all this. At the least, he does finally salute the Cyber-Brigadier — an act that he never did for Alistair when he was alive. In response, Alistair just bows his head.

The Doctor and Clara end up lying to each other

In keeping with most Doctor Who season finales, this episode is a weird mish-mash of dodgy plot points and love saving the day and genuine, earned emotional resolutions. But what really elevates "Death in Heaven," in particular, is the fact that it pays off all of the thematic and character arcs that have been building up throughout the entire season.

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We've never had a year of Doctor Who like this one, in which a single theme had such careful development and deepening, ending with a payoff. (The closest I can think of is the final season of the classic series, in which the notion of "Survival of the Fittest" is raised a lot in "Ghost Light" and a bit elsewhere, before being center stage of the finale, "Survival.")

And yes, the thematic payoff was not particularly subtle — but the massive signposting didn't at all detract from its effectiveness.

The other thing that rescues "Death in Heaven" from some dodgy bits (like the notion that the whole world voted to make an alien in fancy dress its emergency president, in advance) is the understated final sequence, in which Peter Capaldi and Jenna Coleman both convey a ton of emotion with just their faces and body language.

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The story about Clara and the Doctor both confronting the limits of the Doctor's callousness ends with the two of them lying to each other. Before she died, Missy told the Doctor the coordinates where he could find Gallifrey, and swore she wasn't lying for once. (These were its original coordinates, as first mentioned in "Full Circle.") But when the Doctor pilots the TARDIS to those coordinates, he finds just empty space — possibly because Gallifrey is still in another dimension? — and he goes mad with grief, pounding the TARDIS console.

But the Doctor claims he found Gallifrey, because he believes that Clara is happily reunited with Danny and he shouldn't intrude in their lives any more. Meanwhile, Clara starts to tell the Doctor the truth, but when she hears he's found Gallifrey, she decides to lie and tell him that she's back with Danny and everything is fine. It's sort of an O. Henry thing — they each believe the other has what they've wanted, so they each step aside. They end by hugging, which as the Doctor says, is just a way to hide your face.

Clara thanks the Doctor for making her feel special, and he thanks her for "the same" — then he's gone. But halfway through the credits, the story stops, because Santa Claus (Nick Frost) intervenes, insisting that things need to be set right between the Doctor and Clara. Which... should be interesting, I guess.