The more I think about it, the more the Doctor's actions at the very end of this episode piss me off.
They spend two episodes trying to convince prejudiced humans (and by extension, the audience) that the "gangers" are functionally real human beings with the right to life and freedom - regardless of whether or not there's a human plugged into them controlling them.
So what does the Doctor do? He frigging LIQUIFIES ganger-Amy. Without even telling her of his suspiscions beforehand or trying to help her to come to terms with it.
Nevermind that her ganger may have been capable of independent thought and action and might have wanted to live.
Nevermind that keeping the ganger alive might have been a way to trace back the psychic link between it and the real Amy.
Nevermind that killing the ganger opened Amy up to the absolute horror of imprisonment in a tiny chamber, suddenly pregnant and in labor with the implication that she has been raped (forced pregnancy on an unwilling or unknowing host is still rape, regardless of the method).
For once in my life I'm sad to say that I don't like the Doctor at all, and wouldn't ever consider travelling with him.
I see what you saying, but on reflection, I think this is the whole point of these two episodes, and this is why:
- The Doctor went to island knowing the Flesh was there, in its "earliest form". He knew something was up with Amy from the negative/positive pregnancy scan, had a theory about Amy being a Ganger and perhaps even knew how to disrupt her form.
- He did want to do this until he was sure of what he was dealing with, so the visit was to a little research into the Flesh technology and expand his knowledge before acting on his thoughts about Amy
- "Shenanigans" occurred, making up most of parts 1 & 2, including the fact the Flesh in its earliest form had life in its own right.
- At the end, the Doctor drops the remaining 2 off at the company Morpeth Jetsan, urging them to tell them about the Flesh and do something about it - perhaps redevelop the techonology to eliminate this "life potential" from it, leaving it purely as a vehicle for a human controller in dangeous situations, as originally intended.
- The Doctor has deduced Ganger Amy is later "Flesh" technology, following the changes made to eliminate the "life potential" and now knows, following his little trip + "shenanigans" that he can safely "melt" Ganger Amy without killing any sentient life, or chance of it.
- In this context, it is a very Doctor thing to do - don't risk harm to a living organism if you can possibly help it.
- The events in the TARDIS at the end of the episode are the whole point of the rest of the passed 2 episodes - "is it safe to melt Ganger Amy?"