Dalek Sec, partially transformed into a human, steps forward and announces the experiment's success. He orders other humans brought forward for hybridization but the Doctor interrupts. The Daleks explain how they fled through time after the last Dalek/Cyberman war in the 21st century. Sec boasts that he now has human emotions: hostility, anger, hate. The Doctor uses a radio to emit a blast of high-pitched noise to distract the Daleks and their pig slaves so he can get Martha and the others to safety. They get to the surface and return to Hooverville, while the three “normal” Daleks question Sec’s newfound transformation and the fact they don’t trust him.
Solomon tries to rally the men at Hooverville but the pig slaves attack. The men manage to hold them off but two Daleks arrive and blast apart the camp. Solomon confronts them, saying that they’re all outcasts and they should work together. The Daleks ruthlessly gun him down and the Doctor steps forward and offers his life if they’ll stop the attack. The Dalek prepares to exterminate him but Sec overrides it, ordering the Doctor to be brought to him alive.
Back at the Dalek HQ, the Sec hybrid admits that killing Sec was wrong and that they are at the end of their rope. They have been unable to reproduce as Daleks, and he shows the Doctor an army of humans that have been mind-wiped and are ready to be implanted with the Dalek genotype. The Doctor notes that it would require enormous power that they don’t have, but Sec is confident. Back at the camp, Martha figures out that Daleks are using the Empire State Building’s mooring mast to generate power using strips of Dalekenium.
Sec explains to the Doctor that they plan to use an upcoming solar flare to transfer the energy through the Dalekenium to their human army and infuse them with Dalek DNA. However, he plans to make them more human and pleads earnestly with the Doctor to help them and use the TARDIS to take the new “humanized” Daleks to their own planet to find a home for themselves. The other Cult of Dalek members protest but as their leader Sec overrides them.
Using the Doctor’s psychic paper, Martha gets herself, Frank, and Tallulah into the Empire State Building and head for the top floor. They find the plans and determine where the Daleks ordered the addition of the Dalekenium strips. The Doctor goes to work with the Daleks’ genetic equipment, and secretly talks with Laszlo, who the Daleks still believe is mind-controlled.
With the solar flare approaching, the Doctor completes his work but the Daleks override Sec and imprison him. They boast that the human “blanks” will receive full Dalek DNA and their human factor will be eliminated. The Doctor and Laszlo manage to get to the elevator and head up to the top floor, but they fail to stop the elevator from returning to Dalek HQ. With six minutes remaining, the Dalek goes out on the mast to remove the strips while Martha and the others prepare to stop the pig slaves that are coming back up the elevator. Aware that he is dying because the pig slave modifications cause burnout, Laszlo begins to weaken. Martha uses some metal piping and extends it from the outside to the elevator, where the lightning strikes and electrocutes the pig slaves as they arrive.
At the same time, the Doctor loses his sonic screwdriver and fails to remove the last Dalekenium strip. The lightning flows through him and into the building, energizing the Daleks’ new human army and transforming them into Dalek-Humans. The “true” Daleks order them to march through the sewers and bring them more humans for transformation while the imprisoned Sec looks on.
The Doctor goes to Tallulah’s theater with the others and activates his sonic screwdriver, attracting the Daleks’ attention. Dalek Caan hooks into the war machine and sends the troops and the two remaining Daleks to eliminate their greatest enemy. They take the manacles Sec along with them and confront the Doctor. Sec tries to tell his fellow Cult members that they are doomed if they follow the path of death and destruction but they ignore him and try to kill the Doctor. Sec leaps into the beam, giving his life to save his former mortal enemy. The Doctor taunts the Daleks to order their newly-created army to kill him and they do so. The humans hesitate and then start to question their orders. The Doctor reveals that since the lightning passed through him, the Dalek-Humans have a bit of Time Lord DNA, enough to allow them to maintain their individuality. The Daleks open fire on the humans and kill a few, but the rest return fire and destroy the two Daleks. Furious, Caan sends a signal which causes all of the Dalek-Humans to die instantly.
Furious, the Doctor goes back to confront Caan but still offers him one last chance, as one last survivor to another. Caan refuses and slips through time to escape him. Martha and the others bring in the dying Laszlo and the Doctor refuses to lose one more life, and manages to save him using the Daleks’ genetic equipment.
Frank manages to find a place for the partially-transformed Laszlo in Hooverville as they start to rebuild. The Doctor and Martha slip off to the TARDIS where the Doctor notes that they’ll meet the Daleks again some day.