Chapter three – Humanity is a state of mind
"Why should I?"
The Doctor was getting frustrated "Why should you? Why should you go after the man who has been your only friend in the entire world? When you've just realized who you are, and he's confused because you're acting as if he doesn't exist?"
"Yes, he was a good friend, and flatmate, while I was human. But now I am not. I'd prefer to stay here, study the ship, and perhaps attempt to replicate it so that I can travel on my own and continue my research."
"Your research?" The Doctor asked "You were eight when your family sent you from Gallifrey, how can you have research?"
The Chemist scoffed "I may have been human, but my mind certainly wasn't idle. I've been researching the human race. Finding out every fault, every strength, now that I've regained the rest of my brilliant mind, I'll be able to further understand them."
All of this sparked an idea to the Doctor "Then why not stay with John? Study him, continue your business, use the flat for experiments-"
"Unnecessary, all the equipment I need I already have, and the flat is cramped, it would much better suit me to conduct my research here."
"But it would be better for him." The Doctor said. It would, so much better for John if Sherlock was still around. They needed each other to stay a part of the normal world. "And for you. You've just been told about the war, you want to make someone pay for it. I can tell, I've been the same way. But it doesn't work like that. You can't just throw your suffering onto someone else. The best you can do. The best you can ever do, is distract yourself from the pain." The Doctor's expression had gone very grim, bad memories ran through his head at top speed. And he remembered everything bad. And why he needed his companions. Because they were all he had to distract himself.
"I don't need distractions." The Chemist said coldly
"Your research is a distraction! A way of keeping yourself occupied and not thinking of everything horrible that has ever happened!" The Doctor shouted "So you can take whatever equipment you need, but you are going back to John!"
"And you plan on making me do this how?" The Chemist asked, regarding the Doctor with a mix of disbelief and sarcasm.
"If you don't go back to John, I'm not allowing your continued study of the human race."
The Chemist merely smirked "Not allowing? And what exactly do you plan on doing to stop it?"
The Doctor smiled, because for all his knowledge, the Chemist hadn't been around to hear about the Doctor. The oncoming storm, the destroyer of worlds, the monster that had escaped the perfect prison.
"You will stay here as a prisoner, your will have no access to my equipment, or any room besides your own, and this one. You may be clever, but you're nothing without the correct tools, your mind will sit idle, and you'll probably go mad after several days. Is that clear enough?" The Doctor asked
"Crystal." The Chemist said stiffly.
"Well alright then. Get what you need and I'll take you back to the flat."