I took against the Mutant Phase when I first heard it. So much so that that was 2000 and its only now in 2006 that I’ve gone back to listen to it again. My problem centred around the resolution. I recalled Nyssa saying that what happened didn’t make sense and the Doctor gave a reply along the lines of "no it didn’t – it’s a time paradox – they don’t make sense". It seemed to me the ultimate cop out. A story which had progressed 95% of the way and then couldn’t be concluded. So everything went to hell and some sort of reset button was pressed. Throw in a glib reference to temporal paradoxes and all will be well. I found this more annoying than usual with the Mutant Phase. Perhaps it was the writer (through the Doctor) coming out and admitting that his story didn’t work or just the apparent arrogance of the thing.

Six years on and I’ve forgiven the Mutant Phase because I think it actually does make sense. The problem with messing around with time is that you risk changing the future which caused you to change the past in the first place. Like the man who goes from 2006 to the 1920s and kills Hitler before he does any real damage. The death of Hitler means the 2006 he came from never happened, there never was a need to go back in time and so he never went back. The standard Doctor Who idea of the web of time would (most of the time) have us believe that the "correct" version of history would thus repair itself and Hitler would survive.

The Mutant Phase would seem to fall into a similar trap. A future is established where the mutants and not the Daleks are the dominant life form. The Emperor goes back in time and his actions mean that the future we’ve seen doesn’t then happen. Thus is should be that the Emperor never needs to go back in time and so is never present at the critical point and never intervenes.

Here is my take on why the Hitler example and the Mutant Phase differ and why one cannot happen while the other can.

The Daleks create a time corridor from the year 4000 (which isn’t really 4000 but its near enough and is easier to remember) to 2150 (again, not precise but it is the year engrained by the movie). The Doctor gets caught in that time corridor and is propelled to 2150 where Nyssa gets stung by a genetically modified wasp. Everything else that happens – principally the Dalek getting stung – would’ve happened with or without the Doctor being there.

He then leaves, ends up back in the time corridor, and is taken to 4000 where he and the Daleks’ scientific allies attempt to solve the riddle of the mutant phase. With the help of Nyssa’s sting-wound they are able to deduce exactly what caused the mutation. This only happened because the Doctor was there.

They then go back through the time corridor to 2150 and, using the knowledge gained by the Doctor and Nyssa, the Emperor tries to cure the mutant phase. Had this worked then a Hitler paradox would’ve occurred – the Emperor would not have gone back to cure something that in the new time line didn’t happen. But the key thing is that the Doctor realises that the Daleks in 2150 have already discovered the problem and will solve it themselves if the Emperor can be prevented from helping them. The Doctor stops him, they cure it themselves (without any foreknowledge) and the entire mutant phase time line ceases to have ever existed. The Doctor and Nyssa are back in the Tardis and on their way to wherever they were going before the time corridor caught them.

So the prevention of the mutant phase time line cannot be wiped out by the changing of that time line because the decisive action was an omission rather than an addition. By not doing anything, the Emperor might as well not have been there at all. And, thanks to history rewriting itself, he wasn’t. Or isn’t.

The conversation at the end of the episode – normally the point at which things become clearer – actually seems to be deliberately trying to make things more complicated. Witness this key exchange between Nyssa and the Doctor.

"You forced the Dalek Emperor to realise he was the one who caused the mutant phase"

"Yes"

"That doesn’t make sense".

My point is that it DOES make sense because the events are essentially the same in both versions of history – in the "wrong" version the Doctor convinces the Emperor not to interfere. In the "correct" version the Doctor and the Emperor aren’t there to interfere. The end result in both cases is that the Emperor doesn’t interfere. If I can paraphrase The King Maker, "the details change but the end remains the same".

The only part which doesn’t make sense is the question of how the Emperor managed to create the "wrong" time line in the first place as it is established that the Daleks time corridor isn’t really up to the job of transporting people back in time with that degree of accuracy. We can only assume he got lucky and went back with the supposed antidote. Except that the antidote wouldn’t exist without the Doctor and Nyssa. Perhaps the Daleks and their allies synthesised another antidote. One that would be just as ineffective. It is a stretch but it is plausible.

So after six years of disliking the Mutant Phase because it didn’t bother to make sense I now find myself disliking it because it refuses to believe it does make sense. However, there is the old showbiz expression – never work with children, animals or temporal paradoxes and I might be entirely wrong about everything above. Except that I don’t like the Mutant Phase. That still stands regardless.