So, any other show with any other hero probably would have portrayed the Ganger Doctor as an antagonist that needed to be dealt with. But this is Doctor Who, and the Doctor doesn’t swing that way.
See, the Ganger Doctor did absorb everything there was about being the Doctor, but that means all the previous incarnations as well, showing him painfully cycling through famous speeches and catch phrases and even speaking in the voice of some of the more well-known Doctors. And the original Doctor…offers to help him.
See, they really are both the Doctor when you get right down to it, and the Doctor is always there to help. And while most incarnations of the Doctor don’t seem to get along too well with other incarnations, this is the current incarnation getting along with the current incarnation. The biggest problem seems to be Amy who insists to know which one is which, finally settling on the fact the original Doctor ruined his shoes with acid and getting the Ganger to go by the frequent Doctor alias of “John Smith”.
Amy is kinda rude to that guy.
Rory, meanwhile, is trying to be nice to Ganger Jennifer, but it turns out she’s the most bloodthirsty and angry of all the Gangers, tricking Rory into leading the other humans and the Doctor into a room where a lot of acid is due at any moment. The thing is…Ganger Doctor seems to play along with Ganger Jennifer, but he really was just buying time to prove to another Ganger that he loves his human self’s son because…well, they’re all just people, and as the Doctor says at the end of the episode, most people are basically good.
He even proved it because he and his Ganger double had switched shoes. Amy mostly wanted to just know which one was which. She didn’t want either of them to get hurt.
Granted, he’s still the Doctor and he’s still heroic, so when the time comes, he does use the sonic screwdriver to stop Monster Ganger Jennifer after she decided to kill everybody while the original Doctor got all the remaining survivors to safety. That Ganger Dad will go take care of his human son because the human version died, other humans will testify that the Gangers are alive, and the Doctor and his companions get into the TARDIS to leave as Amy goes into labor despite not looking the slightest bit pregnant.
Turns out the Doctor didn’t go to that factory by chance. He’d been trying to scan Amy for a while to see if she was pregnant but the tests came back inconclusive. It seems Amy had been kidnapped and taken away at some point by a mysterious woman with an eyepatch that Amy finally admitted she kept seeing because…this Amy was a Ganger all along. The real Amy is in a white room giving birth, unsure where she is or how she got there. The Doctor wanted a better idea of how the Flesh worked, and now that he knows, he destroys Ganger Amy so he and Rory can go rescue Original Amy.
Someone is really going to regret taking Amy away, methinks…