Joanna telling the story of the vampire known only as "Weird Harold". Harold had gone into a state of hibernation to recover from injury, but a building was built over his resting place. He was trapped underneath the building for years, fully conscious and desperately trying to claw his way out until an earthquake occurred and several vampires had found him among the rubble. Harold's mind was completely destroyed—he's completely driven by the need to hunt, kill and feed, to the point where the other vampires keep him locked away. Joanna even expresses fear that she and her fellow vampires will eventually over time become just like him.
The Doctor's companion Compassion is transformed into a sentient TARDIS through a series of unfortunate events. She's more powerful than the Doctor's old TARDIS, and is armed. That's not the scary thing though, that's the fact her entire internal dimensions are mapped on her own mindscape. She doesn't have much of an imagination until she becomes a TARDIS where everything becomes metaphorical. She also doesn't have much compassion (her name is intentionally ironic). She still dreams though, and her dreams become part of her internal dimensions. One dream is behind a door called "that dream about Fitz"; all we hear is Fitz's screams from behind the door. She makes the Doctor and Fitz live in the part of her that is "the dark side of her mind" because she hates the Doctor because he's a Time Lord (and innately tries to control her) and pities Fitz because he's human. At one point she dumps shoes on Fitz's head with no reason given. All of her internal dimensions are described as dark, haunted and shadowed. Then at one point she warms the breeze that haunts the console room to warm and soothe Fitz, so everything else is either intentional or just because of her apathy.
Now let's talk The Ancestor Cell, which was scary partially because it featured the Doctor dealing with The Virus (in the form of Faction biodata from a failed attempt to take over a sentient ecosystem), partially because a Faction agent cheerfully murders a Time Lord young rebel who'd been sucked into a Faction voodoo cult as a sacrifice to bring one of the Faction's Fathers out of the Vortex, partially because that selfsame Faction agent was proud of having repeatedly murdered her own father by travelling back in time, killing him, setting the destination dial on the time machine back a few hours, and killing him again, and partially because they rape Gallifrey's history. Several times.
And let's not forget how the Paradox biodata virus leads to the Doctor facing the version of himself who will exist because of said virus; Grandfather Paradox, the personification of the god of Faction Paradox, a bald, one-armed man dressed in bone armour, described by Fitz as "the Doctor if he'd spent twenty years in the navy before becoming a psycho".
The (theoretically) Affably Evil villain rips the Doctor's heart out of his chest bare-handed. The villain in question has hands the size of hams and ripped the Doctor's heart out of his chest while he was awake and screaming. Previously this villain wasn't much of an antagonist; this scene comes shortly after he was the best man at the Doctor's wedding, which makes it so much worse.
