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It's still Manhattan. There are still Daleks. They attempt to create a race of Daleks in human bodies, using the Empire State Building as a lightning rod. Dalek Sec is now part human, which the other Daleks really don't like.
The Doctor throws himself in the way of the lightning and, in what will be a continuing theme throughout this series, screams in absolute agony. His plan works, and the resulting Daleks in human corpses become Time Lord / Dalek hybrids in human corpses instead. The Doctor is delighted at having created a new species. He also notices that Dalek Sec is developing human emotions, and offers to find some way to heal him and help him overcome his Dalek-ness forever.
The new hybrid species and Dalek Sec are killed off by the rest of the Cult, and two of the remaining pure Daleks die in the process. Dalek Caan escapes to series 4. Laszlo is kept alive by the Doctor using the Daleks' genetics lab, although he'll be half pig forever. Talullah doesn't mind too much.
- Absurdly Spacious Sewer
- Big Applesauce: Tallulah says that "if aliens had to come to Earth, no wonder they came here" while looking breathlessly at the Manhattan skyline. Of course, the funny thing is that many, many more have targeted London and Cardiff.
- Bond Villain Stupidity: The Doctor standing on the backs of the theatre seats, staring straight at the Daleks who are inexplicably not shooting him despite the fact that he more or less asked them to, could be the poster image for this Trope.
- Close Knit Community: The Hooverville
- Continuity Nod: Although they don't use the terms 'the Dalek/Human Factor', the plot concept of the Daleks wanting to imbue humans with the Dalek nature and the Doctor wanting to imbue Daleks with the human nature is very reminiscent of "The Evil of the Daleks".
- Disney Death: The Doctor.
- Half-Human Hybrid
- Heel Face Turn: After Becoming a half human hybrid, Dalek Sec changes his plans for earth, and instead opts to recreate the Daleks all a half humans instead of full daleks in human form. He convinces the Doctor to prepare for the gamma storm that will give the new Race life and pleads for use of his TARDIS to take them to a planet so they can begin anew. Sadly It dosen't work as Dalek Caan and the other two betray him at the last minute, switch the transformation to full Dalek and capture and Sec.
- Heroic Sacrifice: From Dalek Sec, of all people.
- Humanity Is Infectious: Dalek Sec.
- Humans Are Bastards: Cited as Dalek Sec's motivation for combining himself with a human--now he can feel man's hatred, ambition, and propensity for war.
- Humans Are Special: The Doctor's counter argument to Dalek Sec by pointing out the human mind has so much more potential than simply destroying other forms of life. This leads to Humanity Is Infectious.
- Landmarking the Hidden Base
- Lightning Can Do Anything: Gamma lightning, apparently.
- Nice Job destroying the last of your race, Dalek Caan.
- Pig Man
- Plummet Perspective: Subverted. The sonic screwdriver falls far, but not as far as it looks.
- Redemption Equals Death
- Sedgwick Speech: Here's a hint: never try to appeal to a Dalek's compassion.
- Spikes of Villainy: Dalek DNA is shown this way.
- Technicolor Science
- Tragic Villain: Guess.
- Wasteland Elder
- Whoopi Epiphany Speech: Subverted as the aforementioned Sedgwick Speech.
- X of the Daleks: First time the classic title format for Dalek episodes shows up in the new series.