The Doctor's Sonic Screwdriver was able to collect faint traces of a coding, Greg and Jory ran it through UNIT's programming, and they found that it was sort of like a driver that is commonly found in computers alike. It allowed the Plague Doctor to speak in a way that many wouldn't be able to understand sans the affected ravens, but audio equipment would easily pick it up as interference. With some alternation, the code was rewrote so it would translate whatever the Plague Doctor said and the Doctor had them download the translator to an ear piece that he could easily wear.
The Doctor had decided to try something that he knew would be risky. He was going to talk things over with the Plague Doctor, understand his plight and hopefully find out details about Sofia Lamb and the Corporation. Sherlock and the others would join him, as added support in case things don't go the way that it should. The Doctor silently hoped as he stuck the earpiece in his right ear that he could at least get some conversation out of the Plague Doctor.
"Um, Doctor, I have a question," John raised his hand. The Doctor looked at him. John cleared his throat, "After all this, what's going to happen to us?"
"Indeed, what will happen to us?" Sherlock questioned. The Doctor sighed. "I'll return you to your proper universe a day after I took you," he said.
"Will we remember this?" John asked him. The Doctor didn't respond. Sherlock tilted his head, "Will we?"
Again, the Doctor didn't respond. Clara gave them a generic answer that they accepted as they readied for what would be considered the final confrontation. In truth, both she and the Doctor know what will happen when Sherlock and John return to their universe. It was a sad truth that had its benefits, but the duo will slowly but surely forget they were ever in the TARDIS the moment they are returned. It wouldn't be instant, but by the second hour, the duo wouldn't even recognize them. It was a time-y whime-y thing, the Doctor would say. As long as they were in the TARDIS, they'd remember whatever happened during their time inside, but it also meant if they were outside the TARDIS for too long, they'd forget. Clara and past companions managed to keep their memories due to circumstances, but for Sherlock and John, given that their universe never even heard of the Daleks, it was ideally that they'd forget what they experienced.
The Doctor did want to tell them, but he knew from experience that if he told anyone they'd forget that they even met him, they'd try everything in their power to prevent that from happening. It was better for all of them to keep blissfully ignorant.
Meanwhile, in the Oval Room, Bradley and Moya received a transmission from the higher ups after the revelation. They were to exterminate the Plague Doctor, one way or another. The higher ups deemed him a threat. When asked about imprisoning the Plague Doctor instead, the higher ups replied that imprisoning something like the Plague Doctor would be impossible, not because of his height but solely because of his ravens which now apparently are part of him and meant even touching one would incite his wrath. Bradley asked if they were to include the Doctor on the matter, but the higher ups denied, proclaiming that the Doctor would've hampered with the mission. With that, transmission ended and both Bradley and Moya had to decide how they would exterminate the Plague Doctor without the Doctor or his companions knowing what they were doing.
They both decided that despite what the Plague Doctor had done, he had the justification of killing Walker, and he had never laid a hand on anyone else but Walker. He was to have a swift and painless death, the Plague Doctor; he would be allowed to speak with the Doctor as a courtesy, so UNIT will learn more about the Corporation and what Sofia Lamb had been doing. When the Plague Doctor is done, UNIT will converge and give him a swift death.
Bradley and Moya knew their ramifications for going behind the Doctor's back, but they were under orders from the higher ups and even the Doctor knew better. He knew they had to follow orders to the letter and they couldn't have a say in the matter or do anything. The plan would be for UNIT soldiers to guard the Doctor and his companions as he and they track down and speak with the Plague Doctor. When everything is discussed, they are to open fire with modified rounds that would cause fatal electric shocks upon impact, the soldiers had to keep on target and make sure that the Plague Doctor goes down dead. They had to be swift as the Plague Doctor would respond quickly. Once the Plague Doctor was decreed dead, his body or what remains would be further destroyed by incineration. Then the following morning UNIT will collect the ravens with amber eyes and have them destroyed as well. "He knew the risks," Bradley reminded Moya. Moya nodded and then asked, "Did it have to come to this?"