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There's a lot going on in the episode: there's a T. rex in the Thames, then a flaming T. rex carcass in the Thames; dastardly droids and organ harvesting; and a hot air balloon made of human skin (we're spared a close-up). Yet somehow the biggest shock comes from meeting the Twelfth Doctor (Peter Capaldi). Audience stand-in—and scapegoat—Clara Oswald (Jenna-Louise Coleman), the Doctor's companion, doesn't instantly click with her "new" pal. She wonders why he had to change and if he can change back.
It's clear that, as our proxy, Clara's recalcitrance represents last year's public outcry over the casting of Capaldi, a middle-aged Scotsman; some fans deemed him too old to play a 2000-year-old extraterrestrial. Clara is reminded that the Doctor's previously youthful incarnation was a calculation meant to allay fears (humanity's xenophobia and his own fear of rejection), and that he was "never [her] boyfriend." Take that, fanboys and girls (note: executive producer Steven Moffat wrote the episode).
It's not all finger wagging; eventually the Doctor and Clara bond again and resume the business of fending off yet another alien invasion. But first, their separation highlights their strengths and weaknesses. Clara delivers an appropriately sassy response to Vastra's (Neve McIntosh) accusations of shallowness, and later parlays her physical weakness into the upper hand during a negotiation with the episode's villain, the head of the Clockwork Droids (a species first seen in 2006's "The Girl in the Fireplace"). It's a nice development, given that Clara was mostly a plot device in the previous season.
Meanwhile, the Doctor's superior intelligence and physiology, as mirrored by the "control node" droid, are seen as liabilities. Both the Doctor and the droid have pieced together—literally, in the droid's case—a semblance of humanity. But the droid has been programmed to repair itself with whatever is available; its human appearance is incidental, not intentional. The Doctor, on the other hand, has chosen to appear as disarmingly "normal" as possible.* He seems to be in hiding.
That is, until now—the Twelfth Doctor is all silver hair, austere suits, and "attack eyebrows." He's swapped the charming blathering for bluntness, the comforting companionship for something more challenging. But despite making a conscious sartorial change, the Doctor is at a loss for why he's "wearing" a face he's seen before. And that's what makes "Deep Breath" an effective reset for the series: we don't know much about this new Doctor, and neither does he.
*(Relax, nerds. I know it's far more likely in the Who universe for humans to look like Time Lords, not t’other way around).