The Almost People is a tale of humanity lost and found. As Jen, the Ganger we had most sympathy with last week is driven by her desire for revenge to become more and more monstrous, Cleeve, the human who was most monstrous last week, acknowledges her vulnerability and comes good. The other Gangers reluctantly agree to Jen's plan to destroy the humans, believing it to be their only chance of survival.
The Doctor trusts his Ganger immediately, but Amy finds she can't. She does, however, confide in him about the future Doctor's death, possibly hoping that it was the Ganger who died. She also tells the Doctor about Weird Eyepatch Woman, although the Doctor initally dismisses this as "just a Time Memory". Rory finds two Jens, and a fight breaks out between them, ending with one of them falling into a pool of acid and dissolving, revealing her to be a Ganger. When the surviving Jen shows Rory the pile of discarded Gangers, we are reminded that the Gangers do have a genuine grievance against the humans, but then we discover that the real Jen is dead. Her Ganger, having created another Ganger of herself for the purpose of destroying it to trick Rory into helping her, has crossed a line even by her own standards.
Rory and one of the Doctors have been captured by the Gangers, and base is heading for destruction, with the remaining Doctor and the surviving humans strugging to contain the acid, when Adam's son phones for his birthday. Adam's Ganger goes to get his original, only to find him dying. Being the Human who found it easiest to identify with his Ganger, Adam then hands his life over to his duplicate. The other Gangers no longer support Jen, and help the surviving humans to escape.
At the end, some of the survivors are humans and some are Gangers. We discover that the Doctors had switched boots earlier, so presumably the real Doctor knows about his assasination now. Although the Ganger Doctor and the Ganger Cleeve were dissolved stopping the now completely monstrous Jen, the possiblity that they could reconstitute themselves is left open. But ther's a bigger revalation left to come.
You remember there was a thowaway line last week about how the Flesh could even duplicate clothes? Well, I'd been wondering for a while why Amy, who loves dressing up, had been wearing the same outfit all season. It turned out that since Day of the Moon, the Amy we've been seeing has been a Ganger, and that the real Amy was being held prisoner somewhere. This explains why the Tardis couldn't decide whether she was pregnant or not - the Ganger wasn't, the real Amy was. Now, she's about to give birth, while held captive by the Weird Eyepatch Woman.
By the way, did anyone else think that the episode titles should have been the other way round?