The Doctor’s timeline is an interesting tangle. Instead of being the linear timeline that we imagine when we think of ourselves, the Doctor’s timeline intersects, bisects, loops in on itself and is essentially a tangled mess. Doctors from the past have gone further into the future than the present Doctor, and future Doctors may well run into previous incarnations. It is simply one of the fascinating aspects to Doctor Who.
It is also interesting how, when the Doctor regenerates into a new form and meets his enemies for the first time, they automatically recognize him as their enemy. While it can be easy at times to figure out that he is the Doctor, especially if he steps out of the TARDIS or brandishes his sonic screwdriver, that is not always the case. In fact, the Doctor can just appear and find himself as a target.
This leads to the question of how these enemies know that these random beings are the Doctor. It is not as though he is wearing an outfit that proclaims his status as the Doctor by having question marks everywhere on his wardrobe; at least, not any more. Add in his different mannerisms, and it would be difficult to see how the Doctor’s foes would immediately see through the new features and know who he is.
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Unless, of course, as their time line remains relatively linear, the Doctors of past, present, and future continually intersect and cross into those lines. The past generations of these entities would then be able to warn the future about what form Death would take, as the Doctor would be a different being each time. With such a warning, it would hypothetically be possible to get the drop on the Time Lord, especially if he does not realize that others know who he is.
Obviously, this advance knowledge has yet to work, as the Doctor has not been upgraded, exterminated, or otherwise harmed immediately after a regeneration. While some Doctors may have a much shorter time than others, we have yet to see one last only a couple of episodes before being forced into another regeneration. Clearly, the Doctor’s enemies, while knowing what he will look like, have been unable to use that to their advantage.