Lord Sec, as a new Human Dalek, orders the other humans to be brought forth for hybridization. However, the Doctor interrupts and they immediately recognize him. They explain how they escaped the previous devastation with an emergency time shift but the Doctor is not impressed. He forces Lord Sec to admit he's feeling all of the human emotions… the negative ones. The Doctor uses a radio on a high pitch to distract them so he can get the captive humans away. They run into Tallulah as the Daleks recover and give pursuit with their pig slaves. The semi-transformed Laszlo follows behind his would-be masters.
The Doctor and the others get away to the surface and two of the untransformed Daleks question Lord Sec's plan and express their doubts about his plan. At Hooverville, the pig slaves attack while the Doctor and the rest try to defend themselves. However, two of the Daleks fly in and blast away. Solomon tries to get through to them as fellow outcasts, but the Daleks gun him down. Furious, the Doctor steps forward and dare them to kill him in return for letting the others go. Lord Sec overrides them, saying he wants the Doctor alive.
The Doctor is brought back to the Dalek headquarters where Dalek Sec explains it was wrong to kill Solomon. The human-hybrid then explains that their previous experiments to reproduce failed so they stole thousands of human beings and wiped their minds to create a new race of salves. The Doctor warns they don't have enough power to revive them all but Lord Sec is confident they do.
Martha figures out that the Daleks must be using Dalekenium as a power conductor and talk to Frank to find out that most of the work has been going on at the Empire State Building. Meanwhile, Dalek Sec explains that the DNA in his body was to be used as a template and gamma radiation generated by a solar flare was to be drawn into the energy conductor atop the Empire State Building and their army will awake. Sec tries to convince the Doctor that it wants to regain emotions that their creator stripped them of. The other three Daleks protest but Sec overrides them.
Using the Doctor's psychic papers, Martha gets herself, Frank, and Tallulah past the guards at the Empire State Building. Sec appeals to the Doctor to improve their experiment and notes that the other three Daleks must obey him, which they confirm. Sec asks the Doctor to use the TARDIS to take them to a new home so they can start again, but notes that the pig slaves have a limited lifespan.
At the top of the building, Martha finds the plans and tries to determine what was added more recently. The Doctor starts to modify the Dalek program and notices Laszlo in with the others. Laszlo wonders if the Doctor trusts them and the Doctor says he does, while the unmodified Daleks listen in.
Tallulah discusses Martha's relationship with the Doctor and admits there's no future for her and Laszlo. The solar flare is imminent and the pig slaves activate the gene infusion into the human experiments. Martha finds new lines added to the mooring mast.
In the Dalek headquarters, the three Daleks override Sec's orders and alter the gene feed. Asserting that Sec is no longer a Dalek, they explain the new bodies will be 100% Dalek. The Doctor and Sec are restrained but Laszlo gets the Doctor into the elevator and they head for the mooring mast. They arrive and meet Martha and the others, but the elevator goes down again before the Doctor can stop it.
They have six minutes before the flare hits so the Doctor climbs up to the mast to remove the Dalekenium. High above the city, he struggles to remove the Dalekenium strips. The Daleks send their pig slaves up to the top on the elevator while Martha and the others prepare to fight. Laszlo prepares to struggle but is clearly weakening, and Martha realizes they can use the approaching lightning storm. She rigs up a series of metal pipes from the outside to the elevator.
Dropping his sonic screwdriver and unable to remove all the strips, the Doctor grabs the mast and holds on. The lightning strikes, electrocuting the pig slaves. The remaining energy flows through the Doctor and into the Daleks' human army. The "true" Daleks order their new Dalek-Humans to assume battle position and go forth to convert the rest of Manhattan's population. Martha and Frank go to the mast and find the Doctor who recovers consciousness, while the Dalek-Humans march through the sewers. A furious Sec looks on as a new Dalek takes command and ties into their war computers.
The Doctor says he needs to draw out their army so he can confront them and decides to use the theater above their headquarters. They go there but Laszlo is still weakening, and the Doctor activates his sonic screwdriver to draw the Daleks' attention. The Doctor tries to send Martha back but she refuses, and the Dalek-Humans march in. The two Daleks burst in with the chained and bound Sec and boast of their plan to transform Earth into New Skaro. The Doctor confronts them and Sec warns his cohorts that they are doomed if they go ahead with their plans. When the Daleks open fire on the Doctor, Sec leaps into the beam and dies. The Doctor appeals to the new Dalek-Human army and dares the Daleks to order them to kill him. The Dalek-Humans order them to shoot but they refuse and question their orders, announcing they're not Daleks. The Doctor points out that his Time Lord DNA was infused and gave them the extra bit of freedom. The Daleks open fire on their errant slaves and kill a few, but the rest return fire and destroy the two Daleks. The remaining Dalek, tied into the war computer, sends a destruct signal destroying the remaining Dalek-Humans.
The Doctor goes to confront the last Dalek, Caan, and offers it one last chance but it makes an emergency temporal shift and escapes. Martha and Tallulah bring the dying Laszlo in and the Doctor refuses to accept one more death. Using the Daleks' genetic equipment, the Doctor saves his life and Frank finds a place for him in Hooverville. The Doctor and Martha go back to the TARDIS and Martha wonders if they'll ever see the Dalek again. The Doctor notes that they'll meet again.