So my idea was that reader is actually a Descender and that their history with our Balladeer is actually much more complex than even he realizes until he's inside Irminsul ♥ Consider this:

You, who feel like it's your fault that Dottore started experimenting on Scara, because you think you accidentally lead the doctor to him. So when you flee and realize that Dottore has taken an interest in the puppet, its this abrupt horror because it's all your fault. Kuni is so innocent, he doesn't understand.

You end up doing this dance with Dottore for months, getting close and chased away. Fighting him for all its worth to keep him as far away from Kuni as possible. But even you don't want to get close to Kuni because that means it'll be easy to grab you both. So you do what they can, drive the doctor (so you think) away from a distance.

But then the incident with the furnace begins and you realize far too late that Dottore can change his appearance like that. You rush to the furnace after figuring out what he intends to do but Dottore's clone cuts you off.

"Oh," both of Dottore's clones you've been fighting for what feels like hours come to an abrupt halt. It takes everything in you to keep yourself from collapsing to your knees to catch your breath.

One of his clones is far more damaged than the other, missing a limb and it looks closer to scrap metal than it does a person any longer. But it feels nothing, not like the exhaustion and pain coursing through your body.

"It looks like he didn't make it."

Your heart catches in your throat and the horror is clear on your face as both clones look out into the distance at the furnace.

"What a pity, he would've been invaluable."

No. No no no no! You did all this and still failed him? Still? No. He has to be alive, he has to—you just need to get up and go get him from the furnace. You can still save him.

But as you turn toward the furnace, forgetting about Dottore, a sharp pain hits the back of your head and you fall limp in his arms, unconscious.

He finally caught you.

You end up thinking Scaramouche died because of you, and that it's your fault. From there Scaramouche finds out that Dottore spent months torturing and experimenting on you until you manage to escape. But the damage is so severe that once you find a place to hide away from him, you fall comatose for weeks in some bottom pit underground, that nobody would think twice about.

He then finds out that all those experiments on him? They had many purposes but the main one? It was to try and kill you. Dottore got all the data he wanted out of you except how to kill you. And he almost perfected the poison that would erode away whatever ability you had that was keeping you alive.

And then he sees it, in a memory. Dottore finds you again and this time he manages to use it on you. An injection that he watches your body try to heal itself as it breaks apart. It's painful, but you manage to flee again but this time you fall comatose for months.

Scaramouche knows that the next time Dottore catches you, that poison will kill you.

But the worst part about all of this? As a Descender he can't erase you from Irminsul. So while Dottore and the world forgets all about him, they continue to remember you.