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The Doctor is so trusting like this, or maybe this is just the prelude of what this face will be like, after the distance of the last one. All that the Master has to do is disguise himself as some sort of alchemical healer – he’s always been good at disguises –, and suddenly the Doctor can’t even think to question anything that he says.
The Master offers him an elixir with the claim that it will help the Doctor recover from his regeneration sickness, and that much is true, but the Doctor has no way of knowing this, and the Master could have just as easily given him something else.
Poisoning the Doctor when he’s already sick would be beneath him, so he refrains from doing that, instead offering the Doctor a mild sedative, to help his synapses settle after the thunderstorm of regeneration. In a way, it’s still a form of poison, as its ultimate function is to cause harm, if only by helping the Doctor be well enough to be worth defeating.
The Master is no longer capable of it, but he remembers it well, the way that his entire body would feel like it was on fire, his brain rearranging itself down to the last neuron. Uncontrolled, it’s like a seizure and just as dangerous, but the process is already starting to slow down, despite the many impediments that the Master threw in the Doctor’s way, or perhaps because of them, as adrenaline is known to be an aid to regeneration.
Naturally, this level of confusion should only last a few minutes, followed by a long period of sleep that could last several hours. The Master had, on a few occasions, been able to force himself to maintain lucidity for a couple of days before he was forced to rest, but the Doctor is apparently quite terrible at regenerating for someone who had already done so a few times.
Having read the UNIT files that he long ago stole while trying to understand what the Doctor was doing on Earth, the Master suspected as much, but seeing it for himself for the first time was something else entirely.
The Doctor drinks the concoction without a single analysis of its content, not taking notice of the sedative, and he doesn’t even check his room for hidden passages.
The Master counts the time for the sedative to take effect, and then gives it one more hour to be sure. When he walks in the room, the Doctor doesn’t stir, oblivious to his presence, even when the Master sits on the edge of his bed.
If he had known how trusting the Doctor would be, he might have given him something stronger, or one of any number of poisons that might be interesting to see the Doctor fight against, knowing how hard a Time Lord truly was to kill in this manner, even when exposed to toxic substances.
Still, he presses his luck, placing a hand on the Doctor’s neck and squeezing it gently. The Doctor cough and moves his head to the side, but he doesn’t try to fight him off, so the Master squeezes a little harder, until he hears the Doctor choking. The Master wonders how far he could go before the Doctor tried to stop him, and if he tried, if he would even be able to.
He releases the pressure, moving his hand to the Doctor’s cheek. It would be no challenge at all to take another regeneration from him now, but he wants the Doctor to have at least a fighting chance.
“Enjoy your last few hours, my dear Doctor,” he says, tracing the Doctor’s lower lip with his thumb.
Maybe he won’t even kill the Doctor, just keep him here, under his control. The Doctor is so trusting now, so helpless, and the Master could place him completely under his control. Maybe he doesn’t need to rule the universe, only this pocket dimension made only for him and the Doctor.