And all it would have taken was like 3-4 lines at the end. Something like:
(after they send the factory leader and the ganger off to see the company) AMY: Does it turn out all right? DOCTOR: Yes. Well, mostly. (quick line why there became 2 strains of Flesh, one that was sentient and was given all the rights of a human and one that was totally dependent on the user's mind)
(before he blows her up) DOCTOR: (his babble about going to get a base reading from the original) This will cut the link with Amy's mind. I hope--I really, really hope you the (sentient strain). And if you're not? I'm sorry, but you need to wake up.
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(after they send the factory leader and the ganger off to see the company)
AMY: Does it turn out all right?
DOCTOR: Yes. Well, mostly. (quick line why there became 2 strains of Flesh, one that was sentient and was given all the rights of a human and one that was totally dependent on the user's mind)
(before he blows her up)
DOCTOR: (his babble about going to get a base reading from the original) This will cut the link with Amy's mind. I hope--I really, really hope you the (sentient strain). And if you're not? I'm sorry, but you need to wake up.