Its been shown in the original series (directly stated in a trial of a timelord) that the Doctor was the Master's intellectual superior, however as Professor Yana, he learned new technologies and abilities. One thing that wasn't made clear is "yana tech" more capable than timelord science, or is it merely different. As evidenced by the doctor understanding the footprint engine, its probable that his abilities still trump the Master's on a level playing field, but the Master may have the ability to hide technologies in ways the Doctor is not able to recognise.
The most important thing that i got the impression of was that firstly that the Doctor knew which timelord survived, and much more importantly that he let the Master go. He seemed apologetic towards the Master as if he had betrayed him, this suggests that possibly either before the war, or during, the Master was somehow used by the Doctor as part of one of his schemes. The fear that Yana was the Master, suggests that maybe he had some reason to suspect the Master might be alive. Alternatively its possible that the Doctor unable to kill the Master, used the chamelon arch on the Master by force to give him a chance at a non-evil existance, and did not know where in history he ended up.
My conclusion about him letting the Master go is based on the fact that i strongly suspect that nobody can take off in the Doctor's Tardis when the doctor has the remote control in his hand. The Master may be a genius, but the Doctor is (A ) a greater genius (B ) guardian of the most capable powerful ship in the universe, therefore likely to have taken extremely good care to prevent anyone from using said Tardis.
It is possible that the Master did outwit the Doctor, but i did get the distinct impression it was the Doctor letting the Master go rather than the other way round.
As an aside, the hidden starting element this season, i actually missed, but then again it hadn't happened yet, however i was right that the Doctor triggered it. If the Doctor had never used the chamelon arch, its possible the Master would have never been released, because Martha would never have removed the perception filter, and so Professor Yana would never have noticed it as important. Its possible he would have eventually opened it but its likely that the tardis would have been the trigger, and that would have been in the Doctor's presence. The long and short of the argument is that the Doctor is responsible for creating the saxon event line albiet in an indirect manner.
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