This entry is going to be about both "Daleks In Manhattan" and "Evolution of the Daleks" since they're actually a single story (continuing the new Doctor Who series practice of not simply calling two-parters "Part I" and "Part II" - though I don't know why they don't do that).
"Daleks In Manhattan" reveals to us where the "Cult of Skaro" disappeared to when they executed an emergency temporal jump after the Dalek-Cyberman war. Poor little Daleks, stranded in New York City during the Great Depression. Somehow (which isn't explained) they take over the Empire State Building construction project. Not only are they modifying the building plans for some nefarious purpose (do Daleks have any other kind of purpose?), they're kidnapping transients from the Hoovervilles and experimenting on them. Dumb ones are crossed with pigs and turned into oinking slaves. Smart ones apparently get a different treatment - the Daleks are trying to modify the genetic structure and resurrect their almost dead species! Though WHY they are trying to do this is beyond me, assuming the Cult of Skaro were aware of Davros' attempts to do something similar. By the end of the episode the Dalek Sek has transgenetically merged with a human to become a hybrid - though, again, I have to wonder how he missed that whole business with the "Human Factor" that the Doctor introduced to Daleks ages ago.
"Evolution of the Daleks" picks up on Sek's plan to merge humans and Daleks. Apparently the leader of the Cult of Skaro is quite an admirer of humanity's ability to survive - while lamenting the "purity" of the Daleks having been their own undoing. Too bad for Sek that the other members of the Cult don't share his "vision" for the future evolution of the Daleks. Somehow (again this is not explained) these FOUR last Daleks have kidnapped and wiped the minds of literally THOUSANDS of human beings. Granted, with the mass migrations of the Great Depression it's likely mass disappearances might go unnoticed, but HOW did they do this, exactly? Plus, Sek says they have other such repositories just like the one under the Empire State Building. Regardless, these people are effectively already dead as human beings - their minds are wiped with no way to put them back. That's probably the ONLY reason the Doctor agrees to actually HELP Sek with his plan to use them for the creation of a hybrid Dalek-Human race, which the Doctor sort of agrees to transplant to somewhere else since Earth can't support two sentient species (so the Doctor says). The problem, though, is the other members of the Cult of Skaro aren't on board with this plan. They don't want touchy-feely Daleks that can dance, and love, and sing. They want human bodies with minds that think like Daleks (you know the drill: obey! exterminate! obey!). When the Doctor realizes the plan to send the Daleks in a kinder, gentler direction is doomed he knows he has to intercept the Gamma Radiation burst from a solar flare from powering the Dalek's transgenic process. He doesn't get the collectors all removed in time and has to take the brunt of the blast - though for a Timelord that's not a big deal. He's absorbed the energy of the time stream before, what's a little gamma radiation? By doing so, though, he introduces just a hint of Gallifreyan traits into the hybrids, enough to give them free will and question the Cult of Skaro's orders. A shoot-out between two of the Cult and the hybrids takes care of those Daleks, but the remaining one triggers a self-destruct signal on the hybrids just before he makes another "emergency temporal jump" to escape.
The supporting characters - the showgirl "Tullulla," her part-piggyfied boyfriend "Laslo," and a couple of Hoovervillians don't add that much to the story, and frankly had the Daleks killed them all it wouldn't have affected the story that much. I didn't think this story really had enough "meat" to be a two-parter, and probably would have been better served as a one-hour episode since they didn't bother to do much in the way of character development anyway (not like the "Planet Hell" story last season, which was excellent!). Compressing it would have also improved the pacing and made it a bit more exciting. I'm guessing, though, the Doctor is going to run into that Dalek again - most likely in the far flung future.