Missy and Clara arrive in medieval times via vortex manipulators. Looking down at the crowd below Missy tells Clara, "You probably want to throw up, don't you? Pick a local." (Meaning someone in the crowd below them.)
Boris: Your fish? The Doctor: I may have ordered ONLINE!
Missy and Clara exchange a few words. The Doctor promptly spins around to face where they are, sees Clara on the balcony, and starts playing... "Pretty Woman"! As for Missy, he introduces her to the crowd of medieval onlookers as "It's the wicked stepmother! Everybody hiss!" In response to which, she obligingly twirls her handkerchief and takes a bow.
Even when captured by Daleks, Missy has time to crack jokes. For example, when Clara declares that the TARDIS is basically indestructible:
Missy: Did the Doctor tell you that? Because you should never believe a man about a vehicle.
Missy relating the story that inspired the creation of her latest way to cheat death. It involved the Doctor surrounded by invisible android assassins and drawing their energy to teleport. Then (because he's the Doctor), he fell into a nest of vampire monkeys, but that's a different story. As she says this Clara is hanging upside down and Missy is making a... pointy stick. The reason? She wants to hunt.
The fact that Missy knows this story implies that she, or at least a version of her prior to this body, was involved in and responsible for said android problem in the first place.
The fact that the worst insult Missy can think of to use for the Doctor is "swot".
Not to mention that it goes into Hypocritical Humour, given that Missy is often seen as more book-smart than the Doctor.
"No, he's the Doctor. He fell into a pit of vampire monkeys."
Missy: He's trapped at the heart of the Dalek empire, he's a prisoner of the creatures who hate him most in the universe, and between us and him is everything the deadliest race in all of history can throw at us. We, on the other hand, have a pointy stick.
Clara: Can I have a stick too? Missy: Make your own stick.
How does Missy test the depth of the Dalek city sewers? She pushes Clara in. (Turns out it's twenty feet/six metres.)
"What are you doing?!" "Murdering a Dalek. I'm a Time Lady, it's our golf."
Given that this is the Doctor, and he carries everything (probably including a kitchen sink at some point!) in his pockets, who knows how long that tea has been there!
The Doctor then asks if they're all up for a game of dodgems (think bumper cars).
"Proposition: Davros is an insane, paranoid genius who has survived among several billion trigger-happy mini-tanks for centuries. Conclusion: I'm definitely having his chair."
Davros having the Daleks scour the entire planet to bequeath unto the Doctor a very particular honour: the only other chair on Skaro.
The circumstances of the moment make it a bit of Black Comedy, but there's the all-too-rare bit of a Dalek being a smartass.
The Doctor: Who is going to tell me that Clara Oswald is really dead? Supreme Dalek:Clara Oswald is not alive.
The Doctor's two greatest arch-enemies finally meet face to face. The result: Missy tells Davros it's a real pleasure, pretends she wants to shake his hand and then pokes him in the eye stalk, effectively making good on her threat in the previous episode.
Making this even funnier is the fact that if you pay attention, it looks like Davros was actually going to shake her hand before she pokes him in the eye!
Hearing "That's a bit weird" in a Dalek voice. (Out-of-character, you can just picture how Nicholas Briggs must've been struggling not to crack up mid-dialogue, delivering such un-Dalek-y lines through his voice modulator.)
The Doctor: You really are dying. Davros: Look at me. Did you doubt it? The Doctor: Yes. Davros: Then we have established one thing only. The Doctor: What? Davros:You... arenot... a good... doctor. [Beat, then both of them break into laughter]
Clara, excited that they've managed to find an adventure, tries to get a high five from the Doctor. It goes about as well as you'd expect:
Clara: Well, go on! Don't leave me hanging!
The Doctor's initial awkward attempts at communicating with the ghosts:
The Doctor: Hello! Did you want to show us this? ...It's very nice!
The Doctor insists he understands sign language... only to realize he deleted it in favor of semaphore.
The Doctor: Someone get me a series of coloured flags.
Even better (for those who DO understand sign language), the first thing he signs to Cass is "You're beautiful." She looks genuinely surprised for a moment. (Later, it happens again when the Doctor unconsciously signs "I love you" to Clara in the TARDIS, though she doesn't appear to notice.)
The Doctor's cue cards for when he puts his foot in his mouth. There are a lot of them, with the best probably being, "It was my fault, I should have known you didn't live in Aberdeen."note A belated apology to SarahJane, perhaps?
The Doctor squeeing about the existence of ghosts while everybody else looks stoic. Clara has to rein him in and remind him that they have lost a crew member.
One of the crew engages in a bit of Gallows Humor after they decide to stay and help the Doctor. "If I die, you know that I will come back to haunt you."
Why the Doctor doesn't have a radio on the TARDIS: whatever song he hears first thing in the morning sticks in his head as an Ear Worm... and he got two weeks of "Mysterious Girl" by Peter Andre ("I was begging for the brush of death's merciful hand."). So he disassembled the radio and used the parts to make a clockwork squirrelnote which makes a brief appearance in the next episode.
The Doctor explains the concept of the Ontological Paradox by breaking the fourth wall and talking about a time he went back in time to meet Beethoven, realized Beethoven had never existed, and then used all his Beethoven records to essentially become Beethoven. Then he says that didn't actually happen; Beethoven was real, and the Doctor met him. "Nice chap. Very intense. Fond of an arm wrestle."
When Clara and Cass get separated, Clara tries loudly whispering for her... before remembering Cass is deaf, resulting in her smacking her own forehead.
Alice maintains her composure through her first ride in the TARDIS despite being a in-universe fangirl of the Doctor. Then, as soon as the Doctor is out of sight, she jumps up and down excitedly while saying "it's bigger on the inside!"
Having just asked once again, "Who wrote Beethoven's Fifth?" by way of "explaining" how his survival boiled down to the bootstrap paradox, the scene cuts to a similar closeup of Twelve as in the episode's opening shot... he wordlessly shrugs. Twelve doesn't have to say a thing to be funny!
The Doctor's sonic screwdriver has never been the most sturdy nor foolproof tool throughout its use... but Twelve's sonic sunglasses have a peculiar fragility... as demonstrated when the Doctor proclaims their incredibly advanced nature to the Vikings, one of whom proceeds to simply take them off his face and snap them in half.
The Doctor:[in the most meek-sounding voice he has ever had] ... Clara ... we're going with the Vikings.
The Doctor giving Clara a spectacular spinning hug, but not before faking her out with a thumbs up of course, gotta keep up the façade.
Also, while he's spinning her around, you can just about notice Clara's facial expression showing something of a mix of befuddled confusion and pleasant surprise. D'awwwww...
The fact that the Doctor is just as surprised to see Clara confirm she's held a sword in battle as the villagers. Did she get into a fight while they were separated during an off-camera adventure, or was he just not paying attention?
The Doctor nicknames the Vikings.
"You're Lofty, you're Daphne, Noggin the Nog, ZZ Top, and you're... um... Heidi."
When one of the Vikings asks why they're using wooden weapons instead of metal ones, the Doctor asks another Viking to answer. This one he has nicknamed "Limpy" because his leg is injured and he is currently mending it. "We can't be trusted with them."
The Doctor giving the Vikings their weapons back for proper training after proudly saying that theory is over... cut to the village on fire.
While the Doctor and Clara are coming to terms with the spectacular failure of the initial training run, Ashildr is behind him trying to corral the village chickens to some success.
The Doctor's ignorance that the baby he has been talking to is Lofty's child.
"Why has Lofty stolen a baby?"
When the Doctor starts translating baby talk, the Vikings are confused. Clara says "he speaks baby" without anything more.
The simple fact that the Doctor defeats the villain by essentially threatening to post an embarrassing video on YouTube, while Clara proves that, even in ancient times, Yakety Sax still makes everything funny.
The Doctor: If I didn't know any better, I'd say this was a robbery.
Ashildr once saved a village from the Scarlet Fever. They rewarded her kindness by trying to drown her for being a witch.
Ashildr: Ungrateful peasants.
The Doctor wearing his Sonic Sunglasses at Night so he can (so he can), um, blunder into things and alert the people Ashildr's robbing.
Sam Swift's literal Gallows Humor as he attempts to stretch out his life with terrible stand-up comedy. The puns are awful, but you laugh anyway. And then he enlists the Doctor to help him because, by his own subsequent admission, he was running out of material.
Sam: Doctor! I'm a robber! [beat] The Doctor: Have you taken anything for it?
The Doctor mentions that he's had an immortal companion before, Captain Jack Harkness.
When they're about to go and question the people on the street, Clara announces that she's the Good Cop while the Doctor is the Bad Cop. The Doctor immediately asks why he always has to be the Bad Cop. Clara points out his eyebrows.
The Doctor threatens Ashildr with the Daleks. While that is a terrifying thought, it's rather funny to think the Daleks would turn up like lap dogs if the Doctor called them.
They like shooting un-Daleky things. What does this street have? Lots of shootable un-Daleky things. They would definitely come if he called. It also gives them another shot to kill him too.
The Doctor interrupts his own Badass Boast threatening the people trapping him when he finds a shovel and starts ranting about the evils of gardening.
The Doctor: You're a gardener? I hate gardening! It's like dictatorship for inadequates! Or, it's dictatorship.
When confronted with a locked wooden door, the Doctor notes you can't use telepathy on doors for the obvious reason they're cranky.
And then it opens only to show him a solid wall, which may mean he's right and it opened to troll him.
"My day can't get any worse. Let's see what we can do about yours!"
When the Doctor finds his clothes all dry and waiting for him. After the Fridge Horror realization that he has been here for a long time, you realize that the first time he came here, he didn't have any clothes to change into...
Serious though the episode's tone may be, the scenes when the matron in the barn interrupts the Doctor's soup are quietly amusing: every time Rassilon sends another emissary, she gets more flustered and unnerved by their increasing authority. By the time Rassilon himself shows up, the poor woman's a nervous wreck.
Ohila's sarcastic attitude towards Rassilon and the High Council provides a small amount of additional comic relief.
Rassilon angrily tells Ohila and the Sisterhood of Karn that they have no business on Gallifrey.
Ohila: I heard the Doctor had come home. One so loves fireworks.
A gunship comes to pull the Doctor out of his childhood home. He ignores them. "What's he doing?" "I think he's finishing his soup." Then the commander of the armies comes down to politely talk to him. He ignores him. Then the High Council comes down to bow to him he ignores them too. It's only when Rassilon himself finally comes down that he decides to talk. Also the Moment of Awesome.
Ohila has to painfully spell things out for Rassilon to get him to go:
Ohila: The Doctor does not blame Gallifrey for the horrors of the Time War. Rassilon: I should hope not. Ohila: He just blames you.
The general of Gallifrey's armies is killed by the Doctor and comes back as a woman. A very attractive woman, to boot. It takes the soldiers a few minutes to get used to it. But the best part is that all her regenerations except the last have been female.
The General: How do you people get by with that massive ego?
"Death is Time Lord for man flu."
The Doctor explaining to Clara that Gallifrey is back.
Clara: But I thought it was stuck in the pocket dimension? The Doctor: It was. They must have gotten it out. Clara: How? The Doctor: Don't know. Didn't ask. It would have made them feel clever.
How is Ashildr sustaining a reality bubble at the end of the universe? "Brilliantly."
Clara's new TARDIS has a glitchy chameleon circuit too. In her case, it looks like a retro-50's style American diner, complete with a restaurant outside the TARDIS itself. It really makes you wonder how common such a fault is.
The Doctor tells Clara of the last time he was in the Cloister: "I was a completely different person in those days. Eccentric, a bit mad. Rude to people." Gee, you think, Doctor?
"Then cocktails with Moses. Then I'm going to invent a flying submarine. Why? Because no one ever has and it's annoying."
The TARDIS has a sign on it telling carol singers they WILL be criticized. Presumably, this means that at least one set of Carol Singers did turn up once, requiring the Doctor to put the sign there!
Right from the start, you get an idea what kind of episode it's going to be when the Doctor is overheard ranting at the TARDIS for giving him holographic antlers.
Hologramatic antlers, actually!
"If either of you uses my name again, I shall remove your organs in alphabetical order. Any questions?" "Which alphabet? Oh. You weren't actually looking for questions, were you."
The Doctor has been brought before the dying king, he's surrounded by highly-trained assassins with sentient swords and genetically engineered anger problems and not a lot to do, and millions of people are watching on the monitors. He takes a step back, and says to Nardole:
The Doctor: This might be a disturbing question in context... but you actually think I'm a surgeon? Nardole:[emits a high-pitched whine]
A moment later, when River is calling the Doctor over to start the surgery, he goes back to Nardole again:
The Doctor: Any hint on what species he is, then? Nardole:[high-pitched whine increases in pitch]
A few moments later, the Doctor tells him "don't make puddles."
River nonchalantly telling the Doctor that she plans to kill Hydroflax in order to get the diamond trapped in his head, completely missing the Doctor's WTF expression.
The Doctor: Is this what you're like when I'm not... River: Not what? The Doctor: ...You're talking about murdering someone. River: No I'm not. I'm actually murdering someone.
The Doctor has a sonic screwdriver and sonic sunglasses. Jack had a sonic blaster. Miss Foster had a sonic pen. Sarah Jane had sonic lipstick. River? She's got a sonic trowel (because, after all, she is an archaeologist). One gets the feeling that the whole "sonic device" fad is maybe going a little too far...
Eleven's addiction for fezzes had apparently become so bad by the last time that River saw him that she now carries a fez with her when she is actually murdering someone, just in case the Doctor does turn up.
River has to deal with the Doctor having too much fun during their shenanigans.
River: This is a serious mission in a critical phase. There is nothing to laugh about here. The Doctor: But we're being threatened by a bag! By a head in a bag!
When River produces a wallet which drops down a string of photos chronologically displaying all the Doctor's previous regenerations, the Doctor covertly flips up the bottom panel to make sure that he (or anybody else...) is not there on the back side.
The Doctor:Oh...my....GOD! It's bigger! River: Well, yes. The Doctor: On the inside! River: We need to concentrate. The Doctor: Than it is! River: I know where you're going with this, but I need you to calm down. The Doctor: On the outside! River: You've certainly grasped the essentials. The Doctor: My entire understanding of physical space has been transformed! Three-dimensional Euclidean geometry has been torn up, thrown in the air and snogged to death! My grasp of the universal constants of physical reality has been changed... forever. [beat] Sorry. I've always wanted to see that done properly.
The exchange immediately proceeding said rant is quite funny on its own.
The Doctor:Finally. Ramone: "Finally"? The Doctor:It's my go.
It seems stealing the TARDIS is something River does frequently. The Doctor's expression when he finds out is the icing on the cake. What's funnier still is why River can do this so easily; it's basically mother-daughter time!
The look on his face when River casually reveals that she's discovered the liquor cabinet behind one of the Round Things without him realizing. "Don't tell Dad."
The Doctor's growing exasperation when River is completely oblivious to who he is despite his blatant hints and continually getting interrupted when he tries to tell her never stops being funny.
[after the Doctor explained how the TARDIS works] River: You're very quick! The Doctor: Yes. For a Doctor. River: Yes! [walks off] The Doctor: ...Seriously?
After River gives a tearful and moving speech about how the Doctor is too great to worry about something as minor as her "When you love the Doctor, it's like loving the stars themselves. You don't expect a sunset to admire you back!" Then she looks over at him, and slowly realizes who he is:
The Doctor: Hello, sweetie. River:: ...You are so doing those roots. The Doctor: What, the roots of the sunset? River: Don't you dare. The Doctor: I'll have to check with the stars themselves...
They then go back to their feisty flirty thing within the space of about ten seconds.
Hydroflax (body):What is this conversation? Explain! River: You keep out of this. The Doctor: We need to get to work. River: Okay, what have you got? The Doctor: Four exits, two concealed, one in the ceiling. River: There's also one in the floor. The Doctor: No, I don't like it. River: Too close to the engine ducts? The Doctor: Bit too tight. River: Ooh, I hope you're not being personal. Flemming: Excuse me, what are you talking about? River: Hush, mummy and daddy are busy.
Later, the Doctor asks River what she thinks of the new body. Her response?
River knew about the Harmony and Redemption's ultimate fate thanks to her archaeological background and the book History's Finest Exploding Restaurants. Talk about dining and dashing!
The simple prospect of there being a book titled History's Finest Exploding Restaurants. Either River was yanking Twelve's chain about that part, or it suddenly makes more sense that it'd take an entire planet to house every book ever written in the Whoniverse.
The fact that there are enough exploding restaurants that you can actually fill a book with them.
How many of these exploding restaurants do we want to bet the Doctor and River were involved in, either together or separately? How about all of them?
Even better? The fact it's called History's Finest Exploding Restaurants implies that there are restaurants that have exploded... but not spectacularly enough to be included in said book.
Twelve's complete inability to tell when people look nice or not comes back again.
The Doctor: You look, ah... Amazing? River:[laughing] Doctor, you have no idea whether I look amazing or not. The Doctor: Well, you've... You've moved your hair about, haven't you? River: Well done. It's very sweet of you to try.