Can someone please explain to me the ending of Dr. Who yesterday?

some of us can get real answers because unlike you we paid attention,

ok hears what was happening at some point Amy was kidnapped and replaced with a flesh Ganger (not a "skin" as your calling them) but unlike the Ganger's in the last two episodes her's hadn't been made sentient by the solar storm so she was still controlling it like the others where before the solar storm, so the Amy we where seeing these past few episodes was her in mind and sole just not body (a bit like avatar) the woman Amy kept seeing was the result of her senses picking up bits of her real body's location,

the things we don't know are; who is the women with eye patch? when was Amy kidnapped? who is the farther of her baby? why did the real Amy keep getting pregnant when her ganger didn't? why is some one doing all this?

things that don't make sense are 1)that the doctor killed Amy's ganger even though he says they have some modicum of intelligence even without all the minds a memories of humans, and 2)(the one right question you asked) why didn't the Tardis stabilise her?

I have no idea with the first "thing that doesn't make sense" but I have a few hypnoses for the second one, either it doesn't work on non solar storm ganger or it's not something the tardis just does it's something the doctor made it do for them and not army or the opposite it's something it does do on it's own and but he stopped it from effecting her some how